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Ohya H, Miyake K, Fukuoka H, Oshi M, Ishibe A, Narita K, Kasahara K, Endo I. SLC7A11 and the glutathione pathway as novel prognostic markers in resectable pancreatic ductal adenocarcinoma: A metabolomics study of clinical specimens. Pancreatology 2024; 24:779-786. [PMID: 38866682 DOI: 10.1016/j.pan.2024.05.530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/06/2024] [Accepted: 05/31/2024] [Indexed: 06/14/2024]
Abstract
BACKGROUND/OBJECTIVES Despite the poor prognosis associated with pancreatic ductal adenocarcinoma (PDAC), there remains a lack of clarity regarding the metabolic pathways and their significant impact on its phenotype. Therefore, we aimed to utilize metabolomics to capture changes in clinical PDAC tissues and elucidate the significant metabolic pathways close to its phenotypes. METHODS This basic research was retrospectively validated using database research, immunohistochemistry, and protein analysis based on the findings obtained from metabolomics using clinical tissues collected from prospectively registered patients with PDAC. mRNA expression analysis using a database and protein analysis using archived clinical specimens was performed to validate the candidate pathways identified using metabolomics. Between-group comparisons were analyzed using paired t-tests and log-rank test, and Kaplan-Meier curves illustrated survival times. RESULTS Patients subjected to metabolomics revealed a significant increase in glutathione disulfide levels in PDAC tissues when compared to normal pancreatic tissues. The Cancer Genome Atlas database analysis revealed significant changes in glutathione pathway-related mRNAs in PDAC compared to that in the normal pancreas. Protein analysis of previously resected specimens demonstrated a significant increase in SLC7A11 expression in PDAC tissues. The abundance ratio of SLC7A11 isoforms was associated with the post-operative prognosis in resectable PDAC. CONCLUSION Glutathione disulfide levels were significantly increased in clinical PDAC metabolomics. Additionally, increased mRNA and protein expression in SLC7A11 was observed in PDAC. Furthermore, the SLC7A11 isoform abundance ratio may be a valuable prognostic marker in patients with resectable PDAC.
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Affiliation(s)
- Hiroki Ohya
- Department of Gastroenterological Surgery, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Kentaro Miyake
- Department of Gastroenterological Surgery, Yokohama City University, Yokohama, Kanagawa, Japan.
| | - Hironori Fukuoka
- Department of Gastroenterological Surgery, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Masanori Oshi
- Department of Gastroenterological Surgery, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Atsushi Ishibe
- Department of Gastroenterological Surgery, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Koji Narita
- Chitose Laboratory Corp., Kawasaki, Kanagawa, Japan
| | - Ken Kasahara
- Chitose Laboratory Corp., Kawasaki, Kanagawa, Japan
| | - Itaru Endo
- Department of Gastroenterological Surgery, Yokohama City University, Yokohama, Kanagawa, Japan
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Zhang X, Hu J, Li Y, Tang J, Yang K, Zhong A, Liu Y, Zhang T. Gallbladder microbial species and host bile acids biosynthesis linked to cholesterol gallstone comparing to pigment individuals. Front Cell Infect Microbiol 2024; 14:1283737. [PMID: 38529471 PMCID: PMC10962445 DOI: 10.3389/fcimb.2024.1283737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 02/16/2024] [Indexed: 03/27/2024] Open
Abstract
Gallstones are crystalline deposits in the gallbladder that are traditionally classified as cholesterol, pigment, or mixed stones based on their composition. Microbiota and host metabolism variances among the different types of gallstones remain largely unclear. Here, the bile and gallstone microbial species spectra of 29 subjects with gallstone disease (GSD, 24 cholesterol and 5 pigment) were revealed by type IIB restriction site-associated DNA microbiome sequencing (2bRAD-M). Among them (21 subjects: 18 cholesterol and 3 pigment), plasma samples were subjected to liquid chromatography-mass spectrometry (LC-MS) untargeted metabolomics. The microbiome yielded 896 species comprising 882 bacteria, 13 fungi, and 1 archaeon. Microbial profiling revealed significant enrichment of Cutibacterium acnes and Microbacterium sp005774735 in gallstone and Agrobacterium pusense and Enterovirga sp013044135 in the bile of cholesterol GSD subjects. The metabolome revealed 2296 metabolites, in which malvidin 3-(6''-malonylglucoside), 2-Methylpropyl glucosinolate, and ergothioneine were markedly enriched in cholesterol GSD subjects. Metabolite set enrichment analysis (MSEA) demonstrated enriched bile acids biosynthesis in individuals with cholesterol GSD. Overall, the multi-omics analysis revealed that microbiota and host metabolism interaction perturbations differ depending on the disease type. Perturbed gallstone type-related microbiota may contribute to unbalanced bile acids metabolism in the gallbladder and host, representing a potential early diagnostic marker and therapeutic target for GSD.
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Affiliation(s)
- Xinpeng Zhang
- General Surgery Day Ward, Department of General Surgery, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University & The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu, China
| | - Junqing Hu
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University & The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu, China
- The Center of Obesity and Metabolic Diseases, Department of General Surgery, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University & The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu, China
- Medical Research Center, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University & The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu, China
| | - Yi Li
- General Surgery Day Ward, Department of General Surgery, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University & The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu, China
| | - Jichao Tang
- General Surgery Day Ward, Department of General Surgery, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University & The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu, China
| | - Kaijin Yang
- General Surgery Day Ward, Department of General Surgery, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University & The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu, China
| | - Ayan Zhong
- General Surgery Day Ward, Department of General Surgery, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University & The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu, China
| | - Yanjun Liu
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University & The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu, China
- The Center of Obesity and Metabolic Diseases, Department of General Surgery, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University & The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu, China
| | - Tongtong Zhang
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University & The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu, China
- The Center of Obesity and Metabolic Diseases, Department of General Surgery, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University & The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu, China
- Medical Research Center, The Third People’s Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University & The Second Affiliated Hospital of Chengdu, Chongqing Medical University, Chengdu, China
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Chakraborty N. Metabolites: a converging node of host and microbe to explain meta-organism. Front Microbiol 2024; 15:1337368. [PMID: 38505556 PMCID: PMC10949987 DOI: 10.3389/fmicb.2024.1337368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/13/2024] [Indexed: 03/21/2024] Open
Abstract
Meta-organisms encompassing the host and resident microbiota play a significant role in combatting diseases and responding to stress. Hence, there is growing traction to build a knowledge base about this ecosystem, particularly to characterize the bidirectional relationship between the host and microbiota. In this context, metabolomics has emerged as the major converging node of this entire ecosystem. Systematic comprehension of this resourceful omics component can elucidate the organism-specific response trajectory and the communication grid across the ecosystem embodying meta-organisms. Translating this knowledge into designing nutraceuticals and next-generation therapy are ongoing. Its major hindrance is a significant knowledge gap about the underlying mechanisms maintaining a delicate balance within this ecosystem. To bridge this knowledge gap, a holistic picture of the available information has been presented with a primary focus on the microbiota-metabolite relationship dynamics. The central theme of this article is the gut-brain axis and the participating microbial metabolites that impact cerebral functions.
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Affiliation(s)
- Nabarun Chakraborty
- Medical Readiness Systems Biology, CMPN, WRAIR, Silver Spring, MD, United States
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Semnani-Azad Z, Toledo E, Babio N, Ruiz-Canela M, Wittenbecher C, Razquin C, Wang F, Dennis C, Deik A, Clish CB, Corella D, Fitó M, Estruch R, Arós F, Ros E, García-Gavilan J, Liang L, Salas-Salvadó J, Martínez-González MA, Hu FB, Guasch-Ferré M. Plasma metabolite predictors of metabolic syndrome incidence and reversion. Metabolism 2024; 151:155742. [PMID: 38007148 PMCID: PMC10872312 DOI: 10.1016/j.metabol.2023.155742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 11/19/2023] [Accepted: 11/19/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND Metabolic Syndrome (MetS) is a progressive pathophysiological state defined by a cluster of cardiometabolic traits. However, little is known about metabolites that may be predictors of MetS incidence or reversion. Our objective was to identify plasma metabolites associated with MetS incidence or MetS reversion. METHODS The study included 1468 participants without cardiovascular disease (CVD) but at high CVD risk at enrollment from two case-cohort studies nested within the PREvención con DIeta MEDiterránea (PREDIMED) study with baseline metabolomics data. MetS was defined in accordance with the harmonized International Diabetes Federation and the American Heart Association/National Heart, Lung, and Blood Institute criteria, which include meeting 3 or more thresholds for waist circumference, triglyceride, HDL cholesterol, blood pressure, and fasting blood glucose. MetS incidence was defined by not having MetS at baseline but meeting the MetS criteria at a follow-up visit. MetS reversion was defined by MetS at baseline but not meeting MetS criteria at a follow-up visit. Plasma metabolome was profiled by LC-MS. Multivariable-adjusted Cox regression models and elastic net regularized regressions were used to assess the association of 385 annotated metabolites with MetS incidence and MetS reversion after adjusting for potential risk factors. RESULTS Of the 603 participants without baseline MetS, 298 developed MetS over the median 4.8-year follow-up. Of the 865 participants with baseline MetS, 285 experienced MetS reversion. A total of 103 and 88 individual metabolites were associated with MetS incidence and MetS reversion, respectively, after adjusting for confounders and false discovery rate correction. A metabolomic signature comprised of 77 metabolites was robustly associated with MetS incidence (HR: 1.56 (95 % CI: 1.33-1.83)), and a metabolomic signature of 83 metabolites associated with MetS reversion (HR: 1.44 (95 % CI: 1.25-1.67)), both p < 0.001. The MetS incidence and reversion signatures included several lipids (mainly glycerolipids and glycerophospholipids) and branched-chain amino acids. CONCLUSION We identified unique metabolomic signatures, primarily comprised of lipids (including glycolipids and glycerophospholipids) and branched-chain amino acids robustly associated with MetS incidence; and several amino acids and glycerophospholipids associated with MetS reversion. These signatures provide novel insights on potential distinct mechanisms underlying the conditions leading to the incidence or reversion of MetS.
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Affiliation(s)
- Zhila Semnani-Azad
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Estefanía Toledo
- Department of Preventive Medicine and Public Health, University of Navarra, Pamplona, Spain; IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain.
| | - Nancy Babio
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Unitat de Nutrició Humana, Reus, Spain; Institut d'Investigació Sanitària Pere i Virgili, Hospital Universitari Sant Joan de Reus, Reus, Spain.
| | - Miguel Ruiz-Canela
- Department of Preventive Medicine and Public Health, University of Navarra, Pamplona, Spain; IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain.
| | - Clemens Wittenbecher
- Division of Food and Nutrition Sciences, Department of Biology, Chalmers University of Technology, Gothenburg, Sweden.
| | - Cristina Razquin
- Department of Preventive Medicine and Public Health, University of Navarra, Pamplona, Spain; IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain.
| | - Fenglei Wang
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Courtney Dennis
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Amy Deik
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Clary B Clish
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Dolores Corella
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; Department of Preventive Medicine and Public Health, University of Valencia, Valencia, Spain.
| | - Montserrat Fitó
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; IMIM Hospital del Mar Medical Research Institute, Grup de Risc Cardiovascular i Nutrició, Barcelona, Spain.
| | - Ramon Estruch
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; Department of Internal Medicine, Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, Barcelona, Spain.
| | - Fernando Arós
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; Bioaraba Health Research Institute, Osakidetza Basque Health Service, Araba University Hospital, Vitoria-Gasteiz, Spain; University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain.
| | - Emilio Ros
- Lipid Clinic, Department of Endocrinology and Nutrition, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Hospital Clinic, University of Barcelona, Barcelona, Spain.
| | - Jesús García-Gavilan
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Unitat de Nutrició Humana, Reus, Spain.
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Jordi Salas-Salvadó
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain; Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, Unitat de Nutrició Humana, Reus, Spain; Institut d'Investigació Sanitària Pere i Virgili, Hospital Universitari Sant Joan de Reus, Reus, Spain.
| | - Miguel A Martínez-González
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Preventive Medicine and Public Health, University of Navarra, Pamplona, Spain; IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain.
| | - Frank B Hu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Marta Guasch-Ferré
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Public Health and Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), University of Copenhagen, Copenhagen, Denmark.
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Pinilla L, Benítez ID, Gracia-Lavedan E, Torres G, Mínguez O, Vaca R, Jové M, Sol J, Pamplona R, Barbé F, Sánchez-de-la-Torre M. Metabolipidomic Analysis in Patients with Obstructive Sleep Apnea Discloses a Circulating Metabotype of Non-Dipping Blood Pressure. Antioxidants (Basel) 2023; 12:2047. [PMID: 38136167 PMCID: PMC10741016 DOI: 10.3390/antiox12122047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/07/2023] [Accepted: 11/19/2023] [Indexed: 12/24/2023] Open
Abstract
A non-dipping blood pressure (BP) pattern, which is frequently present in patients with obstructive sleep apnea (OSA), confers high cardiovascular risk. The mechanisms connecting these two conditions remain unclear. In the present study we performed a comprehensive analysis of the blood metabolipidome that aims to provide new insights into the molecular link between OSA and the dysregulation of circadian BP rhythmicity. This was an observational prospective longitudinal study involving adults with suspected OSA who were subjected to full polysomnography (PSG). Patients with an apnea-hypopnea index ≥ 5 events/h were included. Fasting plasma samples were obtained the morning after PSG. Based on the dipping ratio (DR; ratio of night/day BP values) measured via 24 h ambulatory BP monitoring, two groups were established: dippers (DR ≤ 0.9) and non-dippers (DR > 0.9). Treatment recommendations for OSA followed the clinical guidelines. Untargeted metabolomic and lipidomic analyses were performed in plasma samples via liquid chromatography-tandem mass spectrometry. Non-dipper patients represented 53.7% of the cohort (88/164 patients). A set of 31 metabolic species and 13 lipidic species were differentially detected between OSA patients who present a physiologic nocturnal BP decrease and those with abnormal BP dipping. Among the 44 differentially abundant plasma compounds, 25 were putatively identified, notably glycerophospholipids, glycolipids, sterols, and fatty acid derivates. Multivariate analysis defined a specific metabotype of non-dipping BP, which showed a significant dose-response relationship with PSG parameters of OSA severity, and with BP dipping changes after 6 months of OSA treatment with continuous positive airway pressure (CPAP). Bioinformatic analyses revealed that the identified metabolipidomic profile was found to be implicated in multiple systemic biological pathways, with potential physiopathologic implications for the circadian control of BP among individuals with OSA.
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Affiliation(s)
- Lucía Pinilla
- Precision Medicine in Chronic Diseases Group, Respiratory Department, University Hospital Arnau de Vilanova and Santa María, Department of Nursing and Physiotherapy, Faculty of Nursing and Physiotherapy, University of Lleida, IRBLleida, 25198 Lleida, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Iván D. Benítez
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Translational Research in Respiratory Medicine Group, Respiratory Department, University Hospital Arnau de Vilanova and Santa María, IRBLleida, 25198 Lleida, Spain
| | - Esther Gracia-Lavedan
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Translational Research in Respiratory Medicine Group, Respiratory Department, University Hospital Arnau de Vilanova and Santa María, IRBLleida, 25198 Lleida, Spain
| | - Gerard Torres
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Translational Research in Respiratory Medicine Group, Respiratory Department, University Hospital Arnau de Vilanova and Santa María, IRBLleida, 25198 Lleida, Spain
| | - Olga Mínguez
- Translational Research in Respiratory Medicine Group, Respiratory Department, University Hospital Arnau de Vilanova and Santa María, IRBLleida, 25198 Lleida, Spain
| | - Rafaela Vaca
- Translational Research in Respiratory Medicine Group, Respiratory Department, University Hospital Arnau de Vilanova and Santa María, IRBLleida, 25198 Lleida, Spain
| | - Mariona Jové
- Department of Experimental Medicine, University of Lleida-Biomedical Research Institute of Lleida (UdL-IRBLleida), 25198 Lleida, Spain
| | - Joaquim Sol
- Department of Experimental Medicine, University of Lleida-Biomedical Research Institute of Lleida (UdL-IRBLleida), 25198 Lleida, Spain
- Institut Català de la Salut, Atenció Primària, 25198 Lleida, Spain
- Research Support Unit Lleida, Fundació Institut Universitari per a la Recerca a l’Atenció Primària de Salut Jordi Gol i Gurina (IDIAPJGol), 08007 Lleida, Spain
| | - Reinald Pamplona
- Department of Experimental Medicine, University of Lleida-Biomedical Research Institute of Lleida (UdL-IRBLleida), 25198 Lleida, Spain
| | - Ferran Barbé
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
- Translational Research in Respiratory Medicine Group, Respiratory Department, University Hospital Arnau de Vilanova and Santa María, IRBLleida, 25198 Lleida, Spain
| | - Manuel Sánchez-de-la-Torre
- Precision Medicine in Chronic Diseases Group, Respiratory Department, University Hospital Arnau de Vilanova and Santa María, Department of Nursing and Physiotherapy, Faculty of Nursing and Physiotherapy, University of Lleida, IRBLleida, 25198 Lleida, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
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Liu Y, Wu Z, Armstrong DW, Wolosker H, Zheng Y. Detection and analysis of chiral molecules as disease biomarkers. Nat Rev Chem 2023; 7:355-373. [PMID: 37117811 PMCID: PMC10175202 DOI: 10.1038/s41570-023-00476-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2023] [Indexed: 04/30/2023]
Abstract
The chirality of small metabolic molecules is important in controlling physiological processes and indicating the health status of humans. Abnormal enantiomeric ratios of chiral molecules in biofluids and tissues occur in many diseases, including cancers and kidney and brain diseases. Thus, chiral small molecules are promising biomarkers for disease diagnosis, prognosis, adverse drug-effect monitoring, pharmacodynamic studies and personalized medicine. However, it remains difficult to achieve cost-effective and reliable analysis of small chiral molecules in clinical procedures, in part owing to their large variety and low concentration. In this Review, we describe current and emerging techniques that detect and quantify small-molecule enantiomers and their biological importance.
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Affiliation(s)
- Yaoran Liu
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Zilong Wu
- Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Texas Materials Institute, The University of Texas at Austin, Austin, TX, USA.
| | - Daniel W Armstrong
- Department of Chemistry & Biochemistry, University of Texas at Arlington, Arlington, TX, USA.
| | - Herman Wolosker
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.
| | - Yuebing Zheng
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, TX, USA.
- Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Texas Materials Institute, The University of Texas at Austin, Austin, TX, USA.
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA.
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7
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Ekmekciu L, Hopfgartner G. Liquid chromatography and differential mobility spectrometry-data-independent mass spectrometry for comprehensive multidimensional separations in metabolomics. Anal Bioanal Chem 2023; 415:1905-1915. [PMID: 36820908 PMCID: PMC10050028 DOI: 10.1007/s00216-023-04602-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/24/2023]
Abstract
The benefits of combining drift time ion mobility (DTIMS) with liquid chromatography-high-resolution mass spectrometry (HRMS) have been reported for metabolomics but the use of differential time mobility spectrometry (DMS) is less obvious due to the need for rapid scanning of the DMS cell. Drift DTIMS provides additional precursor ion selectivity and collisional cross-section information but the separation resolution between analytes remains cell- and component-dependent. With DMS, the addition of 2-propanol modifier can improve the selectivity but on cost of analyte MS response. In the present work, we investigate the liquid chromatography-mass spectrometry (LC-MS) analysis of a mix of 50 analytes, representative for urine and plasma metabolites, using scanning DMS with the single modifiers cyclohexane (Ch), toluene (Tol), acetonitrile (ACN), ethanol (EtOH), and 2-propanol (IPA), and a binary modifier mixture (cyclohexane/2-propanol) with emphasis on selectivity and signal sensitivity. 1.5% IPA in the N2 stream was found to suppress the signal of 50% of the analytes which could be partially recovered with the use of IPA to 0.05% as a Ch/IPA mixture. The potential to use the separation voltage/compensation voltage/modifier (SV/CoV/Mod) feature as an additional analyte identifier for qualitative analysis is also presented and applied to a data-independent LCxDMS-SWATH-MS workflow for the analysis of endogenous metabolites and drugs of abuse in human urine samples from traffic control.
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Affiliation(s)
- Lysi Ekmekciu
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, 1211, Geneva 4, Switzerland
| | - Gérard Hopfgartner
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, 1211, Geneva 4, Switzerland.
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8
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Molecular Landscape of Tourette's Disorder. Int J Mol Sci 2023; 24:ijms24021428. [PMID: 36674940 PMCID: PMC9865021 DOI: 10.3390/ijms24021428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/29/2022] [Accepted: 01/01/2023] [Indexed: 01/12/2023] Open
Abstract
Tourette's disorder (TD) is a highly heritable childhood-onset neurodevelopmental disorder and is caused by a complex interplay of multiple genetic and environmental factors. Yet, the molecular mechanisms underlying the disorder remain largely elusive. In this study, we used the available omics data to compile a list of TD candidate genes, and we subsequently conducted tissue/cell type specificity and functional enrichment analyses of this list. Using genomic data, we also investigated genetic sharing between TD and blood and cerebrospinal fluid (CSF) metabolite levels. Lastly, we built a molecular landscape of TD through integrating the results from these analyses with an extensive literature search to identify the interactions between the TD candidate genes/proteins and metabolites. We found evidence for an enriched expression of the TD candidate genes in four brain regions and the pituitary. The functional enrichment analyses implicated two pathways ('cAMP-mediated signaling' and 'Endocannabinoid Neuronal Synapse Pathway') and multiple biological functions related to brain development and synaptic transmission in TD etiology. Furthermore, we found genetic sharing between TD and the blood and CSF levels of 39 metabolites. The landscape of TD not only provides insights into the (altered) molecular processes that underlie the disease but, through the identification of potential drug targets (such as FLT3, NAALAD2, CX3CL1-CX3CR1, OPRM1, and HRH2), it also yields clues for developing novel TD treatments.
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Lepoittevin M, Giraud S, Kerforne T, Allain G, Thuillier R, Hauet T. How to improve results after DCD (donation after circulation death). Presse Med 2022; 51:104143. [PMID: 36216034 DOI: 10.1016/j.lpm.2022.104143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/29/2022] [Indexed: 11/09/2022] Open
Abstract
The shortage of organs for transplantation has led health professionals to look for alternative sources of donors. One of the avenues concerns donors who have died after circulatory arrest. This is a special situation because the organs from these donors are exposed to warm ischaemia-reperfusion lesions that are unavoidable during the journey of the organs from the donor to the moment of transplantation in the recipient. We will address and discuss the key issues from the perspective of team organization, legislation and its evolution, and the ethical framework. In a second part, the avenues to improve the quality of organs will be presented following the itinerary of the organs between the donor and the recipient. The important moments from the point of view of therapeutic strategy will be put into perspective. New connections between key players involved in pathophysiological mechanisms and implications for innate immunity and injury processes are among the avenues to explore. Technological developments to improve the quality of organs from these recipients will be analyzed, such as perfusion techniques with new modalities of temperatures and oxygenation. New molecules are being investigated for their potential role in protecting these organs and an analysis of potential prospects will be proposed. Finally, the important perspectives that seem to be favored will be discussed in order to reposition the use of deceased donors after circulatory arrest. The use of these organs has become a routine procedure and improving their quality and providing the means for their evaluation is absolutely inevitable.
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Affiliation(s)
- Maryne Lepoittevin
- Unité UMR U1082, F-86000 Poitiers, France; Faculté de Médecine et de Pharmacie, Université de Poitiers, F-86000 Poitiers, France
| | - Sébastien Giraud
- Unité UMR U1082, F-86000 Poitiers, France; Service de Biochimie, Pôle Biospharm, Centre Hospitalier Universitaire, 2 rue de la Milétrie, CS 90577, 86021 Poitiers Cedex, France
| | - Thomas Kerforne
- Unité UMR U1082, F-86000 Poitiers, France; Faculté de Médecine et de Pharmacie, Université de Poitiers, F-86000 Poitiers, France; CHU Poitiers, Service de Réanimation Chirurgie Cardio-Thoracique et Vasculaire, Coordination des P.M.O., F-86021 Poitiers, France
| | - Géraldine Allain
- Unité UMR U1082, F-86000 Poitiers, France; Faculté de Médecine et de Pharmacie, Université de Poitiers, F-86000 Poitiers, France; CHU Poitiers, Service de Chirurgie Cardiothoracique et Vasculaire, F-86021 Poitiers, France
| | - Raphaël Thuillier
- Unité UMR U1082, F-86000 Poitiers, France; Faculté de Médecine et de Pharmacie, Université de Poitiers, F-86000 Poitiers, France; Service de Biochimie, Pôle Biospharm, Centre Hospitalier Universitaire, 2 rue de la Milétrie, CS 90577, 86021 Poitiers Cedex, France
| | - Thierry Hauet
- Unité UMR U1082, F-86000 Poitiers, France; Faculté de Médecine et de Pharmacie, Université de Poitiers, F-86000 Poitiers, France; Fédération Hospitalo-Universitaire « Survival Optimization in Organ Transplantation », CHU de Poitiers, 2 rue de la Milétrie - CS 90577, 86021 Poitiers Cedex, France.
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A Comprehensive Mass Spectrometry-Based Workflow for Clinical Metabolomics Cohort Studies. Metabolites 2022; 12:metabo12121168. [PMID: 36557207 PMCID: PMC9782571 DOI: 10.3390/metabo12121168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/27/2022] Open
Abstract
As a comprehensive analysis of all metabolites in a biological system, metabolomics is being widely applied in various clinical/health areas for disease prediction, diagnosis, and prognosis. However, challenges remain in dealing with the metabolomic complexity, massive data, metabolite identification, intra- and inter-individual variation, and reproducibility, which largely limit its widespread implementation. This study provided a comprehensive workflow for clinical metabolomics, including sample collection and preparation, mass spectrometry (MS) data acquisition, and data processing and analysis. Sample collection from multiple clinical sites was strictly carried out with standardized operation procedures (SOP). During data acquisition, three types of quality control (QC) samples were set for respective MS platforms (GC-MS, LC-MS polar, and LC-MS lipid) to assess the MS performance, facilitate metabolite identification, and eliminate contamination. Compounds annotation and identification were implemented with commercial software and in-house-developed PAppLineTM and UlibMS library. The batch effects were removed using a deep learning model method (NormAE). Potential biomarkers identification was performed with tree-based modeling algorithms including random forest, AdaBoost, and XGBoost. The modeling performance was evaluated using the F1 score based on a 10-times repeated trial for each. Finally, a sub-cohort case study validated the reliability of the entire workflow.
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11
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Kocak OF, Atakay M, Yaman ME, Senol O, Erkayman MH, Esen BS, Salih B. Chemometrics assisted untargeted metabolomic analysis to explore metabolic alterations in chronic urticaria via LC/Q-TOF/MS/MS. Scand J Clin Lab Invest 2022; 82:533-540. [PMID: 36218334 DOI: 10.1080/00365513.2022.2129436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/06/2022] [Accepted: 09/25/2022] [Indexed: 01/05/2023]
Abstract
Chronic urticaria (CU) is a common disease characterized by the development of recurrent itchy blisters and/or angioedema lasting longer than 6 weeks. The evidence-based diagnosis of CU is described in the most recent urticaria guideline. Metabolomics has the potential to offer diagnostic biomarkers for the detection and prognosis of diseases and predict the efficacy and safety of pharmaceutical interventions. Determining the variation in metabolites found in the plasma of CU patients (n = 20) and 20 controls has therefore been the goal of this investigation. Samples were analyzed using liquid chromatography quadrupole time-of-flight mass spectrometry after applying acetonitrile precipitation. For the purpose of identifying and characterizing metabolites, the METLIN database was utilized. According to results, 21 metabolites were found to be significantly (VIP score > 0.7, p < .05 and fold analysis >1.5) altered. Differentiations between each group were successful via both OPLS-DA and ROC analysis. While plasma allantoate, homogentisate, indole acetate, proline, phenylalanine levels decreased in CU patients compared to healthy subjects, tryptophan, spermidine, phenyl pyruvate, oleic acid, lysine, valine, ornithine, histidine, glutamate, leucine, kynurenine, hypoxanthine, tyrosine, glucose, creatine and cortisol levels were significantly increased. Diagnosis of CU could be achieved by evaluating the metabolic profile of patients.
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Affiliation(s)
- Omer Faruk Kocak
- Department of Chemical Technology, Erzurum Vocational Training Collage, Ataturk University, Erzurum, Turkey
| | - Mehmet Atakay
- Department of Chemistry, Faculty of Science, Hacettepe University, Ankara, Turkey
| | - Mehmet Emrah Yaman
- Department of Analytical Chemistry, Faculty of Pharmacy, Atatürk University, Erzurum, Turkey
| | - Onur Senol
- Department of Analytical Chemistry, Faculty of Pharmacy, Atatürk University, Erzurum, Turkey
| | - Merve Hatun Erkayman
- Department of Dermatology, Faculty of Medicine, Atatürk University, Erzurum, Turkey
| | - Busra Solak Esen
- Department of Dermatology, Faculty of Medicine, Atatürk University, Erzurum, Turkey
| | - Bekir Salih
- Department of Chemistry, Faculty of Science, Hacettepe University, Ankara, Turkey
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12
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Kang J, Xue Y, Chen X, Han BZ. Integrated multi-omics approaches to understand microbiome assembly in Jiuqu, a mixed-culture starter. Compr Rev Food Sci Food Saf 2022; 21:4076-4107. [PMID: 36038529 DOI: 10.1111/1541-4337.13025] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 07/21/2022] [Accepted: 07/26/2022] [Indexed: 01/28/2023]
Abstract
The use of Jiuqu as a saccharifying and fermenting starter in the production of fermented foods is a very old biotechnological process that can be traced back to ancient times. Jiuqu harbors a hub of microbial communities, in which prokaryotes and eukaryotes cohabit, interact, and communicate. However, the spontaneous fermentation based on empirical processing hardly guarantees the stable assembly of the microbiome and a standardized quality of Jiuqu. This review describes the state of the art, limitations, and challenges towards the application of traditional and omics-based technology to study the Jiuqu microbiome and highlights the need for integrating meta-omics data. In addition, we review the varieties of Jiuqu and their production processes, with particular attention to factors shaping the microbiota of Jiuqu. Then, the potentials of integrated omics approaches used in Jiuqu research are examined in order to understand the assembly of the microbiome and improve the quality of the products. A variety of different approaches, including molecular and mass spectrometry-based techniques, have led to scientific advances in the analysis of the complex ecosystem of Jiuqu. To date, the extensive research on Jiuqu has mainly focused on the microbial community diversity, flavor profiles, and biochemical characteristics. An integrative approach to large-scale omics datasets and cultivated microbiota has great potential for understanding the interrelation of the Jiuqu microbiome. Further research on the Jiuqu microbiome may explain the inherent property of compositional stability and stable performance of a complex microbiota coping with environmental perturbations and provide important insights to reconstruct synthetic microbiota and develop modern intelligent manufacturing procedures for Jiuqu.
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Affiliation(s)
- Jiamu Kang
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yansong Xue
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Xiaoxue Chen
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, China
| | - Bei-Zhong Han
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
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Irvine HJ, Acharjee A, Wolcott Z, Ament Z, Hinson HE, Molyneaux BJ, Simard JM, Sheth KN, Kimberly WT. Hypoxanthine is a pharmacodynamic marker of ischemic brain edema modified by glibenclamide. Cell Rep Med 2022; 3:100654. [PMID: 35700741 PMCID: PMC9244997 DOI: 10.1016/j.xcrm.2022.100654] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/16/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022]
Abstract
Brain edema after a large stroke causes significant morbidity and mortality. Here, we seek to identify pharmacodynamic markers of edema that are modified by intravenous (i.v.) glibenclamide (glyburide; BIIB093) treatment. Using metabolomic profiling of 399 plasma samples from patients enrolled in the phase 2 Glyburide Advantage in Malignant Edema and Stroke (GAMES)-RP trial, 152 analytes are measured using liquid chromatography-tandem mass spectrometry. Associations with midline shift (MLS) and the matrix metalloproteinase-9 (MMP-9) level that are further modified by glibenclamide treatment are compared with placebo. Hypoxanthine is the only measured metabolite that associates with MLS and MMP-9. In sensitivity analyses, greater hypoxanthine levels also associate with increased net water uptake (NWU), as measured on serial head computed tomography (CT) scans. Finally, we find that treatment with i.v. glibenclamide reduces plasma hypoxanthine levels across all post-treatment time points. Hypoxanthine, which has been previously linked to inflammation, is a biomarker of brain edema and a treatment response marker of i.v. glibenclamide treatment.
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Affiliation(s)
- Hannah J Irvine
- Division of Neurocritical Care and Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Department of Neurology, NYU Langone Health, New York, NY 10016, USA
| | - Animesh Acharjee
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham B15 2TT, UK; Institute of Translational Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TT, UK; NIHR Surgical Reconstruction and Microbiology Research Centre, Birmingham B15 2TT, UK
| | - Zoe Wolcott
- Division of Neurocritical Care and Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Zsuzsanna Ament
- Division of Neurocritical Care and Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - H E Hinson
- Department of Neurology, Oregon Health Sciences University, Portland, OR 97239, USA
| | - Bradley J Molyneaux
- Division of Neurocritical Care, Department of Neurology, Brigham & Women's Hospital, Boston, MA 02115, USA
| | - J Marc Simard
- Department of Neurosurgery, University of Maryland, Baltimore, MD 21201, USA
| | - Kevin N Sheth
- Division of Neurocritical Care, Department of Neurology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - W Taylor Kimberly
- Division of Neurocritical Care and Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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Wang Y, Juan L, Peng J, Wang T, Zang T, Wang Y. Explore potential disease related metabolites based on latent factor model. BMC Genomics 2022; 23:269. [PMID: 35387615 PMCID: PMC8985251 DOI: 10.1186/s12864-022-08504-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 11/17/2022] Open
Abstract
Background In biological systems, metabolomics can not only contribute to the discovery of metabolic signatures for disease diagnosis, but is very helpful to illustrate the underlying molecular disease-causing mechanism. Therefore, identification of disease-related metabolites is of great significance for comprehensively understanding the pathogenesis of diseases and improving clinical medicine. Results In the paper, we propose a disease and literature driven metabolism prediction model (DLMPM) to identify the potential associations between metabolites and diseases based on latent factor model. We build the disease glossary with disease terms from different databases and an association matrix based on the mapping between diseases and metabolites. The similarity of diseases and metabolites is used to complete the association matrix. Finally, we predict potential associations between metabolites and diseases based on the matrix decomposition method. In total, 1,406 direct associations between diseases and metabolites are found. There are 119,206 unknown associations between diseases and metabolites predicted with a coverage rate of 80.88%. Subsequently, we extract training sets and testing sets based on data increment from the database of disease-related metabolites and assess the performance of DLMPM on 19 diseases. As a result, DLMPM is proven to be successful in predicting potential metabolic signatures for human diseases with an average AUC value of 82.33%. Conclusion In this paper, a computational model is proposed for exploring metabolite-disease pairs and has good performance in predicting potential metabolites related to diseases through adequate validation. The results show that DLMPM has a better performance in prioritizing candidate diseases-related metabolites compared with the previous methods and would be helpful for researchers to reveal more information about human diseases.
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Affiliation(s)
- Yongtian Wang
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China. .,Key Laboratory of Big Data Storage and Management Ministry of Industry and Information Technology, Northwestern Polytechnical University, Xi'an, China.
| | - Liran Juan
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jiajie Peng
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China.,Key Laboratory of Big Data Storage and Management Ministry of Industry and Information Technology, Northwestern Polytechnical University, Xi'an, China
| | - Tao Wang
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China.,Key Laboratory of Big Data Storage and Management Ministry of Industry and Information Technology, Northwestern Polytechnical University, Xi'an, China
| | - Tianyi Zang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China.
| | - Yadong Wang
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China.
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15
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Piestansky J, Olesova D, Matuskova M, Cizmarova I, Chalova P, Galba J, Majerova P, Mikus P, Kovac A. Amino acids in inflammatory bowel diseases: Modern diagnostic tools and methodologies. Adv Clin Chem 2022; 107:139-213. [PMID: 35337602 DOI: 10.1016/bs.acc.2021.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Amino acids are crucial building blocks of living organisms. Together with their derivatives, they participate in many intracellular processes to act as hormones, neuromodulators, and neurotransmitters. For several decades amino acids have been studied for their potential as markers of various diseases, including inflammatory bowel diseases. Subsequent improvements in sample pretreatment, separation, and detection methods have enabled the specific and very sensitive determination of these molecules in multicomponent matrices-biological fluids and tissues. The information obtained from targeted amino acid analysis (biomarker-based analytical strategy) can be further used for early diagnostics, to monitor the course of the disease or compliance of the patients. This review will provide an insight into current knowledge about inflammatory bowel diseases, the role of proteinogenic amino acids in intestinal inflammation and modern analytical techniques used in its diagnosis and disease activity monitoring. Current advances in the analysis of amino acids focused on sample pretreatment, separation strategy, or detection methods are highlighted, and their potential in clinical laboratories is discussed. In addition, the latest clinical data obtained from the metabolomic profiling of patients suffering from inflammatory bowel diseases are summarized with a focus on proteinogenic amino acids.
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Affiliation(s)
- Juraj Piestansky
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia; Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Dominika Olesova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Michaela Matuskova
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Ivana Cizmarova
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Petra Chalova
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Jaroslav Galba
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Petra Majerova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Peter Mikus
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia; Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovakia
| | - Andrej Kovac
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.
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Lépine G, Tremblay-Franco M, Bouder S, Dimina L, Fouillet H, Mariotti F, Polakof S. Investigating the Postprandial Metabolome after Challenge Tests to Assess Metabolic Flexibility and Dysregulations Associated with Cardiometabolic Diseases. Nutrients 2022; 14:nu14030472. [PMID: 35276829 PMCID: PMC8840206 DOI: 10.3390/nu14030472] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/16/2022] Open
Abstract
This review focuses on the added value provided by a research strategy applying metabolomics analyses to assess phenotypic flexibility in response to different nutritional challenge tests in the framework of metabolic clinical studies. We discuss findings related to the Oral Glucose Tolerance Test (OGTT) and to mixed meals with varying fat contents and food matrix complexities. Overall, the use of challenge tests combined with metabolomics revealed subtle metabolic dysregulations exacerbated during the postprandial period when comparing healthy and at cardiometabolic risk subjects. In healthy subjects, consistent postprandial metabolic shifts driven by insulin action were reported (e.g., a switch from lipid to glucose oxidation for energy fueling) with similarities between OGTT and mixed meals, especially during the first hours following meal ingestion while differences appeared in a wider timeframe. In populations with expected reduced phenotypic flexibility, often associated with increased cardiometabolic risk, a blunted response on most key postprandial pathways was reported. We also discuss the most suitable statistical tools to analyze the dynamic alterations of the postprandial metabolome while accounting for complexity in study designs and data structure. Overall, the in-depth characterization of the postprandial metabolism and associated phenotypic flexibility appears highly promising for a better understanding of the onset of cardiometabolic diseases.
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Affiliation(s)
- Gaïa Lépine
- Université Clermont Auvergne, INRAE, UMR 1019, Unité Nutrition Humaine, 63000 Clermont-Ferrand, France; (G.L.); (S.B.); (L.D.)
- Université Paris-Saclay, AgroParisTech, INRAE, UMR PNCA, 75005 Paris, France; (H.F.); (F.M.)
| | - Marie Tremblay-Franco
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, 31300 Toulouse, France;
- Axiom Platform, MetaToul-MetaboHUB, National Infrastructure for Metabolomics and Fluxomics, 31300 Toulouse, France
| | - Sabrine Bouder
- Université Clermont Auvergne, INRAE, UMR 1019, Unité Nutrition Humaine, 63000 Clermont-Ferrand, France; (G.L.); (S.B.); (L.D.)
| | - Laurianne Dimina
- Université Clermont Auvergne, INRAE, UMR 1019, Unité Nutrition Humaine, 63000 Clermont-Ferrand, France; (G.L.); (S.B.); (L.D.)
- Université Paris-Saclay, AgroParisTech, INRAE, UMR PNCA, 75005 Paris, France; (H.F.); (F.M.)
| | - Hélène Fouillet
- Université Paris-Saclay, AgroParisTech, INRAE, UMR PNCA, 75005 Paris, France; (H.F.); (F.M.)
| | - François Mariotti
- Université Paris-Saclay, AgroParisTech, INRAE, UMR PNCA, 75005 Paris, France; (H.F.); (F.M.)
| | - Sergio Polakof
- Université Clermont Auvergne, INRAE, UMR 1019, Unité Nutrition Humaine, 63000 Clermont-Ferrand, France; (G.L.); (S.B.); (L.D.)
- Correspondence:
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Olarini A, Ernst M, Gürdeniz G, Kim M, Brustad N, Bønnelykke K, Cohen A, Hougaard D, Lasky-Su J, Bisgaard H, Chawes B, Rasmussen MA. Vertical Transfer of Metabolites Detectable from Newborn's Dried Blood Spot Samples Using UPLC-MS: A Chemometric Study. Metabolites 2022; 12:94. [PMID: 35208170 PMCID: PMC8879569 DOI: 10.3390/metabo12020094] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 02/04/2023] Open
Abstract
The pregnancy period and first days of a newborn's life is an important time window to ensure a healthy development of the baby. This is also the time when the mother and her baby are exposed to the same environmental conditions and intake of nutrients, which can be determined by assessing the blood metabolome. For this purpose, dried blood spots (DBS) of newborns are a valuable sampling technique to characterize what happens during this important mother-child time window. We used metabolomics profiles from DBS of newborns (age 2-3 days) and maternal plasma samples at gestation week 24 and postpartum week 1 from n=664 mother-child pairs of the Copenhagen Prospective Studies on Asthma in Childhood 2010 (COPSAC2010) cohort, to study the vertical mother-child transfer of metabolites. Further, we investigated how persistent the metabolites are from the newborn and up to 6 months, 18 months, and 6 years of age. Two hundred seventy two metabolites from UPLC-MS (Ultra Performance Liquid Chromatography-Mass Spectrometry) analysis of DBS and maternal plasma were analyzed using correlation analysis. A total of 11 metabolites exhibited evidence of transfer (R>0.3), including tryptophan betaine, ergothioneine, cotinine, theobromine, paraxanthine, and N6-methyllysine. Of these, 7 were also found to show persistence in their levels in the child from birth to age 6 years. In conclusion, this study documents vertical transfer of environmental and food-derived metabolites from mother to child and tracking of those metabolites through childhood, which may be of importance for the child's later health and disease.
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Affiliation(s)
- Alessandra Olarini
- Section of Chemometrics and Analytical Technologies, Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark;
| | - Madeleine Ernst
- Section for Clinical Mass Spectrometry, Department of Congenital Disorders, Danish Center for Neonatal Screening, Statens Serum Institut, 2300 Copenhagen, Denmark; (M.E.); (A.C.); (D.H.)
| | - Gözde Gürdeniz
- COPSAC—Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2820 Gentofte, Denmark; (G.G.); (M.K.); (N.B.); (K.B.); (H.B.)
| | - Min Kim
- COPSAC—Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2820 Gentofte, Denmark; (G.G.); (M.K.); (N.B.); (K.B.); (H.B.)
| | - Nicklas Brustad
- COPSAC—Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2820 Gentofte, Denmark; (G.G.); (M.K.); (N.B.); (K.B.); (H.B.)
| | - Klaus Bønnelykke
- COPSAC—Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2820 Gentofte, Denmark; (G.G.); (M.K.); (N.B.); (K.B.); (H.B.)
| | - Arieh Cohen
- Section for Clinical Mass Spectrometry, Department of Congenital Disorders, Danish Center for Neonatal Screening, Statens Serum Institut, 2300 Copenhagen, Denmark; (M.E.); (A.C.); (D.H.)
| | - David Hougaard
- Section for Clinical Mass Spectrometry, Department of Congenital Disorders, Danish Center for Neonatal Screening, Statens Serum Institut, 2300 Copenhagen, Denmark; (M.E.); (A.C.); (D.H.)
| | - Jessica Lasky-Su
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA;
| | - Hans Bisgaard
- COPSAC—Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2820 Gentofte, Denmark; (G.G.); (M.K.); (N.B.); (K.B.); (H.B.)
| | - Bo Chawes
- COPSAC—Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2820 Gentofte, Denmark; (G.G.); (M.K.); (N.B.); (K.B.); (H.B.)
| | - Morten Arendt Rasmussen
- Section of Chemometrics and Analytical Technologies, Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark;
- COPSAC—Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2820 Gentofte, Denmark; (G.G.); (M.K.); (N.B.); (K.B.); (H.B.)
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18
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Castelli FA, Rosati G, Moguet C, Fuentes C, Marrugo-Ramírez J, Lefebvre T, Volland H, Merkoçi A, Simon S, Fenaille F, Junot C. Metabolomics for personalized medicine: the input of analytical chemistry from biomarker discovery to point-of-care tests. Anal Bioanal Chem 2022; 414:759-789. [PMID: 34432105 PMCID: PMC8386160 DOI: 10.1007/s00216-021-03586-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 12/30/2022]
Abstract
Metabolomics refers to the large-scale detection, quantification, and analysis of small molecules (metabolites) in biological media. Although metabolomics, alone or combined with other omics data, has already demonstrated its relevance for patient stratification in the frame of research projects and clinical studies, much remains to be done to move this approach to the clinical practice. This is especially true in the perspective of being applied to personalized/precision medicine, which aims at stratifying patients according to their risk of developing diseases, and tailoring medical treatments of patients according to individual characteristics in order to improve their efficacy and limit their toxicity. In this review article, we discuss the main challenges linked to analytical chemistry that need to be addressed to foster the implementation of metabolomics in the clinics and the use of the data produced by this approach in personalized medicine. First of all, there are already well-known issues related to untargeted metabolomics workflows at the levels of data production (lack of standardization), metabolite identification (small proportion of annotated features and identified metabolites), and data processing (from automatic detection of features to multi-omic data integration) that hamper the inter-operability and reusability of metabolomics data. Furthermore, the outputs of metabolomics workflows are complex molecular signatures of few tens of metabolites, often with small abundance variations, and obtained with expensive laboratory equipment. It is thus necessary to simplify these molecular signatures so that they can be produced and used in the field. This last point, which is still poorly addressed by the metabolomics community, may be crucial in a near future with the increased availability of molecular signatures of medical relevance and the increased societal demand for participatory medicine.
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Affiliation(s)
- Florence Anne Castelli
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
- MetaboHUB, Gif-sur-Yvette, France
| | - Giulio Rosati
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Christian Moguet
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
| | - Celia Fuentes
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Jose Marrugo-Ramírez
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Thibaud Lefebvre
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
- Centre de Recherche sur l'Inflammation/CRI, Université de Paris, Inserm, Paris, France
- CRMR Porphyrie, Hôpital Louis Mourier, AP-HP Nord - Université de Paris, Colombes, France
| | - Hervé Volland
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
| | - Arben Merkoçi
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Stéphanie Simon
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
- MetaboHUB, Gif-sur-Yvette, France
| | - Christophe Junot
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France.
- MetaboHUB, Gif-sur-Yvette, France.
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19
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Devi S, Pasanna RM, Nadiger N, Ghosh S, Kurpad AV, Mukhopadhyay A. Variability of human fasted venous plasma metabolomic profiles with tourniquet induced hemostasis. Sci Rep 2021; 11:24458. [PMID: 34961768 PMCID: PMC8712516 DOI: 10.1038/s41598-021-03665-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/08/2021] [Indexed: 11/17/2022] Open
Abstract
Venous plasma metabolomics is a potent and highly sensitive tool for identifying and measuring metabolites of interest in human health and disease. Accurate and reproducible insights from such metabolomic studies require extreme care in removing preanalytical confounders; one of these is the duration of tourniquet application when drawing the venous blood sample. Using an untargeted plasma metabolomics approach, we evaluated the effect of varying durations of tourniquet application on the variability in plasma metabolite concentrations in five healthy female subjects. Tourniquet application introduced appreciable variation in the metabolite abundances: 73% of the identified metabolites had higher temporal variation compared to interindividual variation [Intra-Class Correlation (ICC) > 0.50]. As such, we recommend tourniquet application for minimal duration and to wait for 5 min with the needle in situ after removing the tourniquet, to reduce hemostasis-induced variability and false flags in interpretation.
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Affiliation(s)
- Sarita Devi
- Division of Nutrition, St. John's Research Institute, St. John's National Academy of Health Sciences, Sarjapur Road, Bangalore, 560034, India
| | - Roshni M Pasanna
- Division of Nutrition, St. John's Research Institute, St. John's National Academy of Health Sciences, Sarjapur Road, Bangalore, 560034, India
| | - Nikhil Nadiger
- Division of Nutrition, St. John's Research Institute, St. John's National Academy of Health Sciences, Sarjapur Road, Bangalore, 560034, India
| | - Santu Ghosh
- Department of Biostatistics, St. John's Medical College and Hospital, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, India
| | - Anura V Kurpad
- Division of Nutrition, St. John's Research Institute, St. John's National Academy of Health Sciences, Sarjapur Road, Bangalore, 560034, India
| | - Arpita Mukhopadhyay
- Division of Nutrition, St. John's Research Institute, St. John's National Academy of Health Sciences, Sarjapur Road, Bangalore, 560034, India.
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20
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Wang T, Tang L, Lin R, He D, Wu Y, Zhang Y, Yang P, He J. Individual variability in human urinary metabolites identifies age-related, body mass index-related, and sex-related biomarkers. Mol Genet Genomic Med 2021; 9:e1738. [PMID: 34293245 PMCID: PMC8404239 DOI: 10.1002/mgg3.1738] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 05/05/2019] [Accepted: 05/22/2019] [Indexed: 12/14/2022] Open
Abstract
Background Metabolites present in human urine can be influenced by individual physiological parameters (e.g., body mass index [BMI], age, and sex). Observation of altered metabolites concentrations could provide insight into underlying disease pathology, disease prognosis and diagnosis, and facilitate discovery of novel biomarkers. Methods Quantitative metabolomics analysis in the urine of 183 healthy individuals was performed based on high‐resolution liquid chromatography–mass spectrometry (LC–MS). Coefficients of variation were obtained for 109 urine metabolites of all the 183 human healthy subjects. Results Three urine metabolites (such as dehydroepiandrosterone sulfate, acetaminophen glucuronide, and p‐anisic acid) with CV183 > 0.3, for which metabolomics studies have been scarce, are considered highly variable here. We identified 30 age‐related metabolites, 18 BMI‐related metabolites, and 42 sex‐related metabolites. Among the identified metabolites, three metabolites were found to be associated with all three physiological parameters (age, BMI, and sex), which included dehydroepiandrosterone sulfate, 3‐methylcrotonylglycine and N‐acetyl‐aspartic acid. Pearson's coefficients demonstrated that some age‐, BMI‐, and sex‐related compounds are strongly correlated, suggesting that age, BMI, and sex could affect them concomitantly. Conclusion Metabolic differences between distinct physiological statuses were found to be related to several metabolic pathways (such as the caffeine metabolism, the amino acid metabolism, and the carbohydrate metabolism), and these findings may be key for the discovery of new diagnostics and treatments as well as new understandings on the mechanisms of some related diseases.
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Affiliation(s)
- Tianling Wang
- Materia Medica Development Group, Institute of Medicinal Chemistry, Lanzhou University School of Pharmacy, Lanzhou, China.,Dingxi Campus of Gansu, University of Traditional Chinese Medicine, Dingxi, China
| | - Lei Tang
- Materia Medica Development Group, Institute of Medicinal Chemistry, Lanzhou University School of Pharmacy, Lanzhou, China
| | - Ruili Lin
- Materia Medica Development Group, Institute of Medicinal Chemistry, Lanzhou University School of Pharmacy, Lanzhou, China
| | - Dian He
- Materia Medica Development Group, Institute of Medicinal Chemistry, Lanzhou University School of Pharmacy, Lanzhou, China.,Gansu Institute for Drug Control, Lanzhou, China
| | - Yanqing Wu
- Materia Medica Development Group, Institute of Medicinal Chemistry, Lanzhou University School of Pharmacy, Lanzhou, China
| | - Yang Zhang
- Materia Medica Development Group, Institute of Medicinal Chemistry, Lanzhou University School of Pharmacy, Lanzhou, China.,School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Pingrong Yang
- Materia Medica Development Group, Institute of Medicinal Chemistry, Lanzhou University School of Pharmacy, Lanzhou, China.,Gansu Institute for Drug Control, Lanzhou, China
| | - Junquan He
- Materia Medica Development Group, Institute of Medicinal Chemistry, Lanzhou University School of Pharmacy, Lanzhou, China.,Gansu Institute for Drug Control, Lanzhou, China
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21
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Comte B, Monnerie S, Brandolini-Bunlon M, Canlet C, Castelli F, Chu-Van E, Colsch B, Fenaille F, Joly C, Jourdan F, Lenuzza N, Lyan B, Martin JF, Migné C, Morais JA, Pétéra M, Poupin N, Vinson F, Thevenot E, Junot C, Gaudreau P, Pujos-Guillot E. Multiplatform metabolomics for an integrative exploration of metabolic syndrome in older men. EBioMedicine 2021; 69:103440. [PMID: 34161887 PMCID: PMC8237302 DOI: 10.1016/j.ebiom.2021.103440] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 05/20/2021] [Accepted: 06/01/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Metabolic syndrome (MetS), a cluster of factors associated with risks of developing cardiovascular diseases, is a public health concern because of its growing prevalence. Considering the combination of concomitant components, their development and severity, MetS phenotypes are largely heterogeneous, inducing disparity in diagnosis. METHODS A case/control study was designed within the NuAge longitudinal cohort on aging. From a 3-year follow-up of 123 stable individuals, we present a deep phenotyping approach based on a multiplatform metabolomics and lipidomics untargeted strategy to better characterize metabolic perturbations in MetS and define a comprehensive MetS signature stable over time in older men. FINDINGS We characterize significant changes associated with MetS, involving modulations of 476 metabolites and lipids, and representing 16% of the detected serum metabolome/lipidome. These results revealed a systemic alteration of metabolism, involving various metabolic pathways (urea cycle, amino-acid, sphingo- and glycerophospholipid, and sugar metabolisms…) not only intrinsically interrelated, but also reflecting environmental factors (nutrition, microbiota, physical activity…). INTERPRETATION These findings allowed identifying a comprehensive MetS signature, reduced to 26 metabolites for future translation into clinical applications for better diagnosing MetS. FUNDING The NuAge Study was supported by a research grant from the Canadian Institutes of Health Research (CIHR; MOP-62842). The actual NuAge Database and Biobank, containing data and biologic samples of 1,753 NuAge participants (from the initial 1,793 participants), are supported by the Fonds de recherche du Québec (FRQ; 2020-VICO-279753), the Quebec Network for Research on Aging, a thematic network funded by the Fonds de Recherche du Québec - Santé (FRQS) and by the Merck-Frost Chair funded by La Fondation de l'Université de Sherbrooke. All metabolomics and lipidomics analyses were funded and performed within the metaboHUB French infrastructure (ANR-INBS-0010). All authors had full access to the full data in the study and accept responsibility to submit for publication.
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Affiliation(s)
- Blandine Comte
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Stéphanie Monnerie
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Marion Brandolini-Bunlon
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Cécile Canlet
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, Toulouse 31300, France
| | - Florence Castelli
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Emeline Chu-Van
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Benoit Colsch
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Charlotte Joly
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Fabien Jourdan
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, Toulouse 31300, France
| | - Natacha Lenuzza
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Bernard Lyan
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Jean-François Martin
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, Toulouse 31300, France
| | - Carole Migné
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - José A Morais
- Division de Gériatrie, McGill University, Center de recherche du Center universitaire de santé McGill, Montreal, Canada
| | - Mélanie Pétéra
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Nathalie Poupin
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, Toulouse 31300, France
| | - Florence Vinson
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, MetaboHUB, Toulouse 31300, France
| | - Etienne Thevenot
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Christophe Junot
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), MetaboHUB, F-91191 Gif sur Yvette, France
| | - Pierrette Gaudreau
- Center de Recherche du Center hospitalier de l'Université de Montréal, Montreal, Canada; Département de médecine, Université de Montréal, Montreal, Canada
| | - Estelle Pujos-Guillot
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France.
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22
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Zhou D, Zhu W, Sun T, Wang Y, Chi Y, Chen T, Lin J. iMAP: A Web Server for Metabolomics Data Integrative Analysis. Front Chem 2021; 9:659656. [PMID: 34026726 PMCID: PMC8133432 DOI: 10.3389/fchem.2021.659656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/06/2021] [Indexed: 12/11/2022] Open
Abstract
Metabolomics data analysis depends on the utilization of bioinformatics tools. To meet the evolving needs of metabolomics research, several integrated platforms have been developed. Our group has developed a desktop platform IP4M (integrated Platform for Metabolomics Data Analysis) which allows users to perform a nearly complete metabolomics data analysis in one-stop. With the extensive usage of IP4M, more and more demands were raised from users worldwide for a web version and a more customized workflow. Thus, iMAP (integrated Metabolomics Analysis Platform) was developed with extended functions, improved performances, and redesigned structures. Compared with existing platforms, iMAP has more methods and usage modes. A new module was developed with an automatic pipeline for train-test set separation, feature selection, and predictive model construction and validation. A new module was incorporated with sufficient editable parameters for network construction, visualization, and analysis. Moreover, plenty of plotting tools have been upgraded for highly customized publication-ready figures. Overall, iMAP is a good alternative tool with complementary functions to existing metabolomics data analysis platforms. iMAP is freely available for academic usage at https://imap.metaboprofile.cloud/ (License MPL 2.0).
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Affiliation(s)
- Di Zhou
- Metabo-Profile Biotechnology (Shanghai) Co. Ltd., Shanghai, China
| | - Wenjia Zhu
- Metabo-Profile Biotechnology (Shanghai) Co. Ltd., Shanghai, China
| | - Tao Sun
- Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Yang Wang
- Metabo-Profile Biotechnology (Shanghai) Co. Ltd., Shanghai, China
| | - Yi Chi
- Metabo-Profile Biotechnology (Shanghai) Co. Ltd., Shanghai, China
| | - Tianlu Chen
- Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Jingchao Lin
- Metabo-Profile Biotechnology (Shanghai) Co. Ltd., Shanghai, China
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23
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Muthubharathi BC, Gowripriya T, Balamurugan K. Metabolomics: small molecules that matter more. Mol Omics 2021; 17:210-229. [PMID: 33598670 DOI: 10.1039/d0mo00176g] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metabolomics, an analytical study with high-throughput profiling, helps to understand interactions within a biological system. Small molecules, called metabolites or metabolomes with the size of <1500 Da, depict the status of a biological system in a different manner. Currently, we are in need to globally analyze the metabolome and the pathways involved in healthy, as well as diseased conditions, for possible therapeutic applications. Metabolome analysis has revealed high-abundance molecules during different conditions such as diet, environmental stress, microbiota, and disease and treatment states. As a result, it is hard to understand the complete and stable network of metabolites of a biological system. This review helps readers know the available techniques to study metabolomics in addition to other major omics such as genomics, transcriptomics, and proteomics. This review also discusses the metabolomics in various pathological conditions and the importance of metabolomics in therapeutic applications.
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24
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Zanin M, Aitya NA, Basilio J, Baumbach J, Benis A, Behera CK, Bucholc M, Castiglione F, Chouvarda I, Comte B, Dao TT, Ding X, Pujos-Guillot E, Filipovic N, Finn DP, Glass DH, Harel N, Iesmantas T, Ivanoska I, Joshi A, Boudjeltia KZ, Kaoui B, Kaur D, Maguire LP, McClean PL, McCombe N, de Miranda JL, Moisescu MA, Pappalardo F, Polster A, Prasad G, Rozman D, Sacala I, Sanchez-Bornot JM, Schmid JA, Sharp T, Solé-Casals J, Spiwok V, Spyrou GM, Stalidzans E, Stres B, Sustersic T, Symeonidis I, Tieri P, Todd S, Van Steen K, Veneva M, Wang DH, Wang H, Wang H, Watterson S, Wong-Lin K, Yang S, Zou X, Schmidt HH. An Early Stage Researcher's Primer on Systems Medicine Terminology. NETWORK AND SYSTEMS MEDICINE 2021; 4:2-50. [PMID: 33659919 PMCID: PMC7919422 DOI: 10.1089/nsm.2020.0003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2020] [Indexed: 12/19/2022] Open
Abstract
Background: Systems Medicine is a novel approach to medicine, that is, an interdisciplinary field that considers the human body as a system, composed of multiple parts and of complex relationships at multiple levels, and further integrated into an environment. Exploring Systems Medicine implies understanding and combining concepts coming from diametral different fields, including medicine, biology, statistics, modeling and simulation, and data science. Such heterogeneity leads to semantic issues, which may slow down implementation and fruitful interaction between these highly diverse fields. Methods: In this review, we collect and explain more than100 terms related to Systems Medicine. These include both modeling and data science terms and basic systems medicine terms, along with some synthetic definitions, examples of applications, and lists of relevant references. Results: This glossary aims at being a first aid kit for the Systems Medicine researcher facing an unfamiliar term, where he/she can get a first understanding of them, and, more importantly, examples and references for digging into the topic.
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Affiliation(s)
- Massimiliano Zanin
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Madrid, Spain
| | - Nadim A.A. Aitya
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - José Basilio
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | - Jan Baumbach
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Arriel Benis
- Faculty of Technology Management, Holon Institute of Technology (HIT), Holon, Israel
| | - Chandan K. Behera
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - Magda Bucholc
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - Filippo Castiglione
- CNR National Research Council, IAC Institute for Applied Computing, Rome, Italy
| | - Ioanna Chouvarda
- Lab of Computing, Medical Informatics, and Biomedical Imaging Technologies, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Blandine Comte
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Tien-Tuan Dao
- Biomechanics and Bioengineering Laboratory (UMR CNRS 7338), Université de Technologie de Compiègne, Compiègne, France
- Labex MS2T “Control of Technological Systems-of-Systems,” CNRS and Université de Technologie de Compiègne, Compiègne, France
| | - Xuemei Ding
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - Estelle Pujos-Guillot
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Nenad Filipovic
- Faculty of Engineering, University of Kragujevac, Kragujevac, Serbia
- Bioengineering Research and Development Center (BioIRC), Kragujevac, Serbia
- Steinbeis Advanced Risk Technologies Institute doo Kragujevac, Kragujevac, Serbia
| | - David P. Finn
- Pharmacology and Therapeutics, School of Medicine, Galway Neuroscience Centre, National University of Ireland, Galway, Republic of Ireland
| | - David H. Glass
- School of Computing, Ulster University, Ulster, United Kingdom
| | - Nissim Harel
- Faculty of Sciences, Holon Institute of Technology (HIT), Holon, Israel
| | - Tomas Iesmantas
- Department of Mathematics and Natural Sciences, Kaunas University of Technology, Kaunas, Lithuania
| | - Ilinka Ivanoska
- Faculty of Computer Science and Engineering, Ss. Cyril and Methodius University, Skopje, Macedonia
| | - Alok Joshi
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - Karim Zouaoui Boudjeltia
- Laboratory of Experimental Medicine (ULB 222), Medicine Faculty, Université libre de Bruxelles, CHU de Charleroi, Charleroi, Belgium
| | - Badr Kaoui
- Biomechanics and Bioengineering Laboratory (UMR CNRS 7338), Université de Technologie de Compiègne, Compiègne, France
- Labex MS2T “Control of Technological Systems-of-Systems,” CNRS and Université de Technologie de Compiègne, Compiègne, France
| | - Daman Kaur
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, Ulster, United Kingdom
| | - Liam P. Maguire
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - Paula L. McClean
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, Ulster, United Kingdom
| | - Niamh McCombe
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - João Luís de Miranda
- Escola Superior de Tecnologia e Gestão, Instituto Politécnico de Portalegre, Portalegre, Portugal
- Centro de Recursos Naturais e Ambiente (CERENA), Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | | | | | - Annikka Polster
- Centre for Molecular Medicine Norway (NCMM), Forskningparken, Oslo, Norway
| | - Girijesh Prasad
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - Damjana Rozman
- Centre for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ioan Sacala
- Faculty of Automatic Control and Computers, University Politehnica of Bucharest, Bucharest, Romania
| | - Jose M. Sanchez-Bornot
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - Johannes A. Schmid
- Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | - Trevor Sharp
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Jordi Solé-Casals
- Data and Signal Processing Research Group, University of Vic–Central University of Catalonia, Vic, Spain
- Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
- College of Artificial Intelligence, Nankai University, Tianjin, China
| | - Vojtěch Spiwok
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - George M. Spyrou
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Egils Stalidzans
- Computational Systems Biology Group, Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Blaž Stres
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Faculty of Civil and Geodetic Engineering, University of Ljubljana, Ljubljana, Slovenia
- Department of Automation, Biocybernetics and Robotics, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Tijana Sustersic
- Faculty of Engineering, University of Kragujevac, Kragujevac, Serbia
- Bioengineering Research and Development Center (BioIRC), Kragujevac, Serbia
- Steinbeis Advanced Risk Technologies Institute doo Kragujevac, Kragujevac, Serbia
| | - Ioannis Symeonidis
- Center for Research and Technology Hellas, Hellenic Institute of Transport, Thessaloniki, Greece
| | - Paolo Tieri
- CNR National Research Council, IAC Institute for Applied Computing, Rome, Italy
| | - Stephen Todd
- Altnagelvin Area Hospital, Western Health and Social Care Trust, Altnagelvin, United Kingdom
| | - Kristel Van Steen
- BIO3-Systems Genetics, GIGA-R, University of Liege, Liege, Belgium
- BIO3-Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Da-Hui Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, and School of Systems Science, Beijing Normal University, Beijing, China
| | - Haiying Wang
- School of Computing, Ulster University, Ulster, United Kingdom
| | - Hui Wang
- School of Computing, Ulster University, Ulster, United Kingdom
| | - Steven Watterson
- Northern Ireland Centre for Stratified Medicine, Ulster University, Londonderry, United Kingdom
| | - KongFatt Wong-Lin
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - Su Yang
- Intelligent Systems Research Centre, School of Computing, Engineering and Intelligent Systems, Ulster University, Ulster, United Kingdom
| | - Xin Zou
- Shanghai Centre for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Harald H.H.W. Schmidt
- Faculty of Health, Medicine & Life Science, Maastricht University, Maastricht, The Netherlands
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Reyes-Garcés N, Boyacı E, Gómez-Ríos GA, Olkowicz M, Monnin C, Bojko B, Vuckovic D, Pawliszyn J. Assessment of solid phase microextraction as a sample preparation tool for untargeted analysis of brain tissue using liquid chromatography-mass spectrometry. J Chromatogr A 2021; 1638:461862. [PMID: 33433374 DOI: 10.1016/j.chroma.2020.461862] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/19/2020] [Accepted: 12/25/2020] [Indexed: 12/14/2022]
Abstract
This work presents an evaluation of solid-phase microextraction (SPME) SPME in combination with liquid chromatography-high resolution mass spectrometry (LC-HRMS) as an analytical approach for untargeted brain analysis. The study included a characterization of the metabolite coverage provided by C18, mixed-mode (MM, with benzene sulfonic acid and C18 functionalities), and hydrophilic lipophilic balanced (HLB) particles as sorbents in SPME coatings after extraction from cow brain homogenate at static conditions. The effects of desorption solvent, extraction time, and chromatographic modes on the metabolite features detected were investigated. Method precision and absolute matrix effects were also assessed. Among the main findings of this work, it was observed that all three tested coating chemistries were able to provide comparable brain tissue information. HLB provided higher responses for polar metabolites; however, as these fibers were prepared in-house, higher inter-fiber relative standard deviations were also observed. C18 and HLB coatings offered similar responses with respect to lipid-related features, whereas MM and C18 provided the best results in terms of method precision. Our results also showed that the use of methanol is essential for effective desorption of non-polar metabolites. Using a reversed-phase chromatographic method, an average of 800 and 1200 brain metabolite features detected in positive and negative modes, respectively, met inter-fibre RSD values below 30% (n=4) after removal of fibre and solvent artefacts from the associated datasets. For features detected using a lipidomics method, a total of 900 and 1800 features detected using C18 fibers in positive and negative mode, respectively, met the same criteria. In terms of absolute matrix effects, the majority of the model metabolites tested showed values between 80 and 120%, which are within the acceptable range. Overall, the findings of this work lay the foundation for further optimization of parameters for SPME-LC-HRMS methods suitable for in vivo and ex vivo brain (and other tissue) untargeted studies, and support the applicability of this approach for non-destructive tissue metabolomics.
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Affiliation(s)
| | - Ezel Boyacı
- Department of Chemistry, University of Waterloo, ON N2L 3G1, Canada
| | | | - Mariola Olkowicz
- Department of Chemistry, University of Waterloo, ON N2L 3G1, Canada
| | - Cian Monnin
- Department of Chemistry and Biochemistry, Concordia University, Montreal QC H4B 1R6, Canada
| | - Barbara Bojko
- Department of Chemistry, University of Waterloo, ON N2L 3G1, Canada
| | - Dajana Vuckovic
- Department of Chemistry and Biochemistry, Concordia University, Montreal QC H4B 1R6, Canada
| | - Janusz Pawliszyn
- Department of Chemistry, University of Waterloo, ON N2L 3G1, Canada.
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Capillary Electrophoresis-Mass Spectrometry for Metabolomics: Possibilities and Perspectives. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1336:159-178. [PMID: 34628632 DOI: 10.1007/978-3-030-77252-9_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Capillary electrophoresis-mass spectrometry (CE-MS) is a very useful analytical technique for the selective and highly efficient profiling of polar and charged metabolites in a wide range of biological samples. Compared to other analytical techniques, the use of CE-MS in metabolomics is relatively low as the approach is still regarded as technically challenging and not reproducible. In this chapter, the possibilities of CE-MS for metabolomics are highlighted with special emphasis on the use of recently developed interfacing designs. The utility of CE-MS for targeted and untargeted metabolomics studies is demonstrated by discussing representative and recent examples in the biomedical and clinical fields. The potential of CE-MS for large-scale and quantitative metabolomics studies is also addressed. Finally, some general conclusions and perspectives are given on this strong analytical separation technique for probing the polar metabolome.
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Hoang Anh N, Min JE, Kim SJ, Phuoc Long N. Biotherapeutic Products, Cellular Factories, and Multiomics Integration in Metabolic Engineering. ACTA ACUST UNITED AC 2020; 24:621-633. [DOI: 10.1089/omi.2020.0112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nguyen Hoang Anh
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Jung Eun Min
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Sun Jo Kim
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Nguyen Phuoc Long
- Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, South Korea
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28
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Narduzzi L, Dervilly G, Audran M, Le Bizec B, Buisson C. A role for metabolomics in the antidoping toolbox? Drug Test Anal 2020; 12:677-690. [DOI: 10.1002/dta.2788] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/30/2020] [Accepted: 03/05/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Luca Narduzzi
- Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA)Oniris, INRAE Nantes France
| | - Gaud Dervilly
- Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA)Oniris, INRAE Nantes France
| | - Michel Audran
- Département des analysesAgence Française de Lutte contre le Dopage (AFLD) Châtenay‐Malabry France
| | - Bruno Le Bizec
- Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA)Oniris, INRAE Nantes France
| | - Corinne Buisson
- Département des analysesAgence Française de Lutte contre le Dopage (AFLD) Châtenay‐Malabry France
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29
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Han K, Kwon O, Jung SY, Park IH, Hwang MS, Park SY, Hwang EH, Lee JH. Jakyakgamcho-tang in the relief of delayed-onset muscle soreness in healthy adults: study protocol for a randomized, double-blind, placebo-controlled, crossover design clinical trial. Trials 2020; 21:211. [PMID: 32085792 PMCID: PMC7035661 DOI: 10.1186/s13063-020-4119-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 01/29/2020] [Indexed: 12/16/2022] Open
Abstract
Background Muscle soreness after exercise, called delayed-onset muscle soreness (DOMS), may cause significant changes in muscle function and may increase the risk of sports injuries. Therefore, various therapeutic strategies have been studied to help recovery after exercise. Jakyakgamcho-tang (JGT) is a widely prescribed herbal medicine to treat muscle pain and cramps in traditional Eastern medicine. The aim of this study is to evaluate the effect of JGT for reducing pain and improving muscle damage after exercise. Methods This study is a randomized, double-blind, placebo-controlled, crossover design clinical trial. A total of 30 healthy male adults will be recruited. Subjects who voluntarily wish to participate in this study will be hospitalized for 4 days. On the first day, the subjects will perform a standardized treadmill exercise for 1 h to induce DOMS. After the exercise, the subjects will take either JGT or a placebo for 3 days. After a more than 1 week wash-out period, the subjects will repeat the same process with the other drug. Pain intensity, calf circumference, and pain threshold will be measured as outcome measures. Blood tests and blood pressure will be measured as safety assessments. In addition, blood tests for muscle damage and inflammation markers, such as creatine kinase, interleukin-6, and C-reactive protein, will be analyzed. Discussion This will be the first trial to assess the effect of JGT on exercise-induced muscle soreness. Our findings will provide valuable data to determine the clinical effects of JGT on DOMS. Trial registration Clinical Research Information Sevice, KCT0003457. Registered on 29 January 2019.
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Affiliation(s)
- Kyungsun Han
- Clinical Medicine Division, Korea Institute of Oriental Medicine, 1672 Yuseong-daro, Yuseong-gu, Daejeon, 34054, Republic of Korea
| | - Ojin Kwon
- Clinical Medicine Division, Korea Institute of Oriental Medicine, 1672 Yuseong-daro, Yuseong-gu, Daejeon, 34054, Republic of Korea
| | - So-Young Jung
- Clinical Medicine Division, Korea Institute of Oriental Medicine, 1672 Yuseong-daro, Yuseong-gu, Daejeon, 34054, Republic of Korea
| | - In-Hwa Park
- Department of Rehabilitation Medicine of Korean Medicine, Spine and Joint Center, Pusan National University Korean Medicine Hospital, Yangsan, 50612, Republic of Korea
| | - Man-Suk Hwang
- Department of Rehabilitation Medicine of Korean Medicine, Spine and Joint Center, Pusan National University Korean Medicine Hospital, Yangsan, 50612, Republic of Korea.,Division of Clinical Medicine, School of Korean Medicine, Pusan National University, Yangsan, 50612, Republic of Korea
| | - Sun-Young Park
- Department of Rehabilitation Medicine of Korean Medicine, Spine and Joint Center, Pusan National University Korean Medicine Hospital, Yangsan, 50612, Republic of Korea
| | - Eui-Hyoung Hwang
- Department of Rehabilitation Medicine of Korean Medicine, Spine and Joint Center, Pusan National University Korean Medicine Hospital, Yangsan, 50612, Republic of Korea. .,Division of Clinical Medicine, School of Korean Medicine, Pusan National University, Yangsan, 50612, Republic of Korea.
| | - Jun-Hwan Lee
- Clinical Medicine Division, Korea Institute of Oriental Medicine, 1672 Yuseong-daro, Yuseong-gu, Daejeon, 34054, Republic of Korea. .,Korean Medicine Life Science, University of Science & Technology (UST), Campus of Korea Institute of Oriental Medicine, Daejeon, 34113, Republic of Korea.
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Potentially Bioactive Metabolites from Pineapple Waste Extracts and Their Antioxidant and α-Glucosidase Inhibitory Activities by 1H NMR. Foods 2020; 9:foods9020173. [PMID: 32053982 PMCID: PMC7073707 DOI: 10.3390/foods9020173] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 12/03/2022] Open
Abstract
Pineapple (Ananas comosus) waste is a promising source of metabolites for therapeutics, functional foods, and cosmeceutical applications. This study strives to characterize the complete metabolite profiles of a variety of MD2 pineapple waste extracts. Metabolomics strategies were utilized to identify bioactive metabolites of this variety prepared with different solvent ratios. Each pineapple waste extract was first screened for total phenolic content, 2,2-diphenyl-1-picrylhydrazyl free radical scavenging, nitric oxide scavenging, and α-glucosidase inhibitory activities. The highest TPC was found in all samples of the peel, crown, and core extracted using a 50% ethanol ratio, even though the results were fairly significant than those obtained for other ethanol ratios. Additionally, crown extracted with a 100% ethanol ratio demonstrated the highest potency in DPPH and NO scavenging activity, with IC50 values of 296.31 and 338.52 µg/mL, respectively. Peel extracted with 100% ethanol exhibited the highest α-glucosidase inhibitory activity with an IC50 value of 92.95 µg/mL. Then, the extracts were analyzed and the data from 1H NMR were processed using multivariate data analysis. A partial least squares and correlogram plot suggested that 3-methylglutaric acid, threonine, valine, and α-linolenic acid were the main contributors to the antioxidant activities, whereas epicatechin was responsible for the α-glucosidase inhibitory activity. Relative quantification further supported that 100% crown extract was among the extracts that possessed the most abundant potential metabolites. The present study demonstrated that the crown and peel parts of MD2 pineapple extracted with 100% ethanol are potentially natural sources of antioxidants and α-glucosidase inhibitors, respectively.
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Bernardo-Bermejo S, Sánchez-López E, Castro-Puyana M, Benito-Martínez S, Lucio-Cazaña FJ, Marina ML. A Non-Targeted Capillary Electrophoresis-Mass Spectrometry Strategy to Study Metabolic Differences in an In vitro Model of High-Glucose Induced Changes in Human Proximal Tubular HK-2 Cells. Molecules 2020; 25:molecules25030512. [PMID: 31991659 PMCID: PMC7037647 DOI: 10.3390/molecules25030512] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 12/13/2022] Open
Abstract
Diabetic nephropathy is characterized by the chronic loss of kidney function due to high glucose renal levels. HK-2 proximal tubular cells are good candidates to study this disease. The aim of this work was to study an in vitro model of high glucose-induced metabolic alterations in HK-2 cells to contribute to the pathogenesis of this diabetic complication. An untargeted metabolomics strategy based on CE-MS was developed to find metabolites affected under high glucose conditions. Intracellular and extracellular fluids from HK-2 cells treated with 25 mM glucose (high glucose group), with 5.5 mM glucose (normal glucose group), and with 5.5 mM glucose and 19.5 mM mannitol (osmotic control group) were analyzed. The main changes induced by high glucose were found in the extracellular medium where increased levels of four amino acids were detected. Three of them (alanine, proline, and glutamic acid) were exported from HK-2 cells to the extracellular medium. Other affected metabolites include Amadori products and cysteine, which are more likely cause and consequence, respectively, of the oxidative stress induced by high glucose in HK-2 cells. The developed CE-MS platform provides valuable insight into high glucose-induced metabolic alterations in proximal tubular cells and allows identifying discriminative molecules of diabetic nephropathy.
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Affiliation(s)
- Samuel Bernardo-Bermejo
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona Km. 33.600, Alcalá de Henares, 28871 Madrid, Spain; (S.B.-B.); (E.S.-L.); (M.C.-P.)
| | - Elena Sánchez-López
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona Km. 33.600, Alcalá de Henares, 28871 Madrid, Spain; (S.B.-B.); (E.S.-L.); (M.C.-P.)
- Instituto de Investigación Química Andrés M. del Río (IQAR), Universidad de Alcalá, Ctra. Madrid-Barcelona Km. 33.600, Alcalá de Henares, 28871 Madrid, Spain
| | - María Castro-Puyana
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona Km. 33.600, Alcalá de Henares, 28871 Madrid, Spain; (S.B.-B.); (E.S.-L.); (M.C.-P.)
- Instituto de Investigación Química Andrés M. del Río (IQAR), Universidad de Alcalá, Ctra. Madrid-Barcelona Km. 33.600, Alcalá de Henares, 28871 Madrid, Spain
| | - Selma Benito-Martínez
- Departamento de Biología de Sistemas, Universidad de Alcalá, Ctra. Madrid-Barcelona Km. 33.600, Alcalá de Henares, 28871 Madrid, Spain; (S.B.-M.); (F.J.L.-C.)
- “Ramón y Cajal” Health Research Institute (IRYCIS), Universidad de Alcalá, 28871 Madrid, Spain
| | - Francisco Javier Lucio-Cazaña
- Departamento de Biología de Sistemas, Universidad de Alcalá, Ctra. Madrid-Barcelona Km. 33.600, Alcalá de Henares, 28871 Madrid, Spain; (S.B.-M.); (F.J.L.-C.)
| | - María Luisa Marina
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona Km. 33.600, Alcalá de Henares, 28871 Madrid, Spain; (S.B.-B.); (E.S.-L.); (M.C.-P.)
- Instituto de Investigación Química Andrés M. del Río (IQAR), Universidad de Alcalá, Ctra. Madrid-Barcelona Km. 33.600, Alcalá de Henares, 28871 Madrid, Spain
- Correspondence: ; Tel.: +34-91-885-4935; Fax: +34-91-885-4971
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Metabolomic and Lipidomic Signatures of Metabolic Syndrome and its Physiological Components in Adults: A Systematic Review. Sci Rep 2020; 10:669. [PMID: 31959772 PMCID: PMC6971076 DOI: 10.1038/s41598-019-56909-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 12/19/2019] [Indexed: 12/20/2022] Open
Abstract
The aim of this work was to conduct a systematic review of human studies on metabolite/lipid biomarkers of metabolic syndrome (MetS) and its components, and provide recommendations for future studies. The search was performed in MEDLINE, EMBASE, EMB Review, CINHAL Complete, PubMed, and on grey literature, for population studies identifying MetS biomarkers from metabolomics/lipidomics. Extracted data included population, design, number of subjects, sex/gender, clinical characteristics and main outcome. Data were collected regarding biological samples, analytical methods, and statistics. Metabolites were compiled by biochemical families including listings of their significant modulations. Finally, results from the different studies were compared. The search yielded 31 eligible studies (2005–2019). A first category of articles identified prevalent and incident MetS biomarkers using mainly targeted metabolomics. Even though the population characteristics were quite homogeneous, results were difficult to compare in terms of modulated metabolites because of the lack of methodological standardization. A second category, focusing on MetS components, allowed comparing more than 300 metabolites, mainly associated with the glycemic component. Finally, this review included also publications studying type 2 diabetes as a whole set of metabolic risks, raising the interest of reporting metabolomics/lipidomics signatures to reflect the metabolic phenotypic spectrum in systems approaches.
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33
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Zoni E, Minoli M, Bovet C, Wehrhan A, Piscuoglio S, Ng CKY, Gray PC, Spahn M, Thalmann GN, Kruithof-de Julio M. Preoperative plasma fatty acid metabolites inform risk of prostate cancer progression and may be used for personalized patient stratification. BMC Cancer 2019; 19:1216. [PMID: 31842810 PMCID: PMC6916032 DOI: 10.1186/s12885-019-6418-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/29/2019] [Indexed: 02/06/2023] Open
Abstract
Background Little is known about the relationship between the metabolite profile of plasma from pre-operative prostate cancer (PCa) patients and the risk of PCa progression. In this study we investigated the association between pre-operative plasma metabolites and risk of biochemical-, local- and metastatic-recurrence, with the aim of improving patient stratification. Methods We conducted a case-control study within a cohort of PCa patients recruited between 1996 and 2015. The age-matched primary cases (n = 33) were stratified in low risk, high risk without progression and high risk with progression as defined by the National Comprehensive Cancer Network. These samples were compared to metastatic (n = 9) and healthy controls (n = 10). The pre-operative plasma from primary cases and the plasma from metastatic patients and controls were assessed with untargeted metabolomics by LC-MS. The association between risk of progression and metabolite abundance was calculated using multivariate Cox proportional-hazard regression and the relationship between metabolites and outcome was calculated using median cut-off normalized values of metabolite abundance by Log-Rank test using the Kaplan Meier method. Results Medium-chain acylcarnitines (C6-C12) were positively associated with the risk of PSA progression (p = 0.036, median cut-off) while long-chain acylcarnitines (C14-C16) were inversely associated with local (p = 0.034) and bone progression (p = 0.0033). In primary cases, medium-chain acylcarnitines were positively associated with suberic acid, which also correlated with the risk of PSA progression (p = 0.032, Log-Rank test). In the metastatic samples, this effect was consistent for hexanoylcarnitine, L.octanoylcarnitine and decanoylcarnitine. Medium-chain acylcarnitines and suberic acid displayed the same inverse association with tryptophan, while indoleacetic acid, a breakdown product of tryptophan metabolism was strongly associated with PSA (p = 0.0081, Log-Rank test) and lymph node progression (p = 0.025, Log-Rank test). These data were consistent with the increased expression of indoleamine 2,3 dioxygenase (IDO1) in metastatic versus primary samples (p = 0.014). Finally, functional experiments revealed a synergistic effect of long chain fatty acids in combination with dihydrotestosterone administration on the transcription of androgen responsive genes. Conclusions This study strengthens the emerging link between fatty acid metabolism and PCa progression and suggests that measuring levels of medium- and long-chain acylcarnitines in pre-operative patient plasma may provide a basis for improving patient stratification.
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Affiliation(s)
- Eugenio Zoni
- Department for BioMedical Research, Urology Research Laboratory, University of Bern, Bern, Switzerland
| | - Martina Minoli
- Department for BioMedical Research, Urology Research Laboratory, University of Bern, Bern, Switzerland
| | - Cédric Bovet
- University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Anne Wehrhan
- University Institute of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Salvatore Piscuoglio
- Institute of Pathology, University Hospital Basel, University of Basel, Basel, Switzerland.,Visceral Surgery Research Laboratory, Clarunis, Department of Biomedicine, University of Basel, Basel, Switzerland.,Clarunis Universitäres Bauchzentrum Basel, Basel, Switzerland
| | - Charlotte K Y Ng
- Visceral Surgery Research Laboratory, Clarunis, Department of Biomedicine, University of Basel, Basel, Switzerland.,Department for BioMedical Research, Oncogenomics, University of Bern, Bern, Switzerland
| | - Peter C Gray
- ScienceMedia Inc, 8910 University Center Ln Suite 400, San Diego, CA, 92122, USA
| | - Martin Spahn
- Zentrum für Urologie Zürich und Prostatakarzinomzentrum Hirslanden ZürichKlinik Hirslanden, Zürich, Switzerland.,Department of Urology, Essen University Hospital, University of Duisburg-Essen, Essen, Germany
| | - George N Thalmann
- Department for BioMedical Research, Urology Research Laboratory, University of Bern, Bern, Switzerland.,Department of Urology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Marianna Kruithof-de Julio
- Department for BioMedical Research, Urology Research Laboratory, University of Bern, Bern, Switzerland. .,Department of Urology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
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Analytic Correlation Filtration: A New Tool to Reduce Analytical Complexity of Metabolomic Datasets. Metabolites 2019; 9:metabo9110250. [PMID: 31653057 PMCID: PMC6918187 DOI: 10.3390/metabo9110250] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 10/21/2019] [Accepted: 10/22/2019] [Indexed: 11/16/2022] Open
Abstract
Metabolomics generates massive and complex data. Redundant different analytical species and the high degree of correlation in datasets is a constraint for the use of data mining/statistical methods and interpretation. In this context, we developed a new tool to detect analytical correlation into datasets without confounding them with biological correlations. Based on several parameters, such as a similarity measure, retention time, and mass information from known isotopes, adducts, or fragments, the algorithm principle is used to group features coming from the same analyte, and to propose one single representative per group. To illustrate the functionalities and added-value of this tool, it was applied to published datasets and compared to one of the most commonly used free packages proposing a grouping method for metabolomics data: 'CAMERA'. This tool was developed to be included in Galaxy and will be available in Workflow4Metabolomics (http://workflow4metabolomics.org). Source code is freely available for download under CeCILL 2.1 license at https://services.pfem.clermont.inra.fr/gitlab/grandpa /tool-acf and implement in Perl.
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Brandolini-Bunlon M, Pétéra M, Gaudreau P, Comte B, Bougeard S, Pujos-Guillot E. Multi-block PLS discriminant analysis for the joint analysis of metabolomic and epidemiological data. Metabolomics 2019; 15:134. [PMID: 31583480 DOI: 10.1007/s11306-019-1598-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/25/2019] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Metabolomics is a powerful phenotyping tool in nutrition and health research, generating complex data that need dedicated treatments to enrich knowledge of biological systems. In particular, to investigate relations between environmental factors, phenotypes and metabolism, discriminant statistical analyses are generally performed separately on metabolomic datasets, complemented by associations with metadata. Another relevant strategy is to simultaneously analyse thematic data blocks by a multi-block partial least squares discriminant analysis (MBPLSDA) allowing determining the importance of variables and blocks in discriminating groups of subjects, taking into account data structure. OBJECTIVE The present objective was to develop a full open-source standalone tool, allowing all steps of MBPLSDA for the joint analysis of metabolomic and epidemiological data. METHODS This tool was based on the mbpls function of the ade4 R package, enriched with functionalities, including some dedicated to discriminant analysis. Provided indicators help to determine the optimal number of components, to check the MBPLSDA model validity, and to evaluate the variability of its parameters and predictions. RESULTS To illustrate the potential of this tool, MBPLSDA was applied to a real case study involving metabolomics, nutritional and clinical data from a human cohort. The availability of different functionalities in a single R package allowed optimizing parameters for an efficient joint analysis of metabolomics and epidemiological data to obtain new insights into multidimensional phenotypes. CONCLUSION In particular, we highlighted the impact of filtering the metabolomic variables beforehand, and the relevance of a MBPLSDA approach in comparison to a standard PLS discriminant analysis method.
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Affiliation(s)
- Marion Brandolini-Bunlon
- Université Clermont Auvergne, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, 63000, Clermont-Ferrand, France.
| | - Mélanie Pétéra
- Université Clermont Auvergne, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, 63000, Clermont-Ferrand, France
| | - Pierrette Gaudreau
- Centre de Recherche du Centre hospitalier de l'Université de Montréal, Montréal, Canada
- Département de médecine, Université de Montréal, Montréal, Canada
| | - Blandine Comte
- Université Clermont Auvergne, INRA, UNH, 63000, Clermont-Ferrand, France
| | | | - Estelle Pujos-Guillot
- Université Clermont Auvergne, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, 63000, Clermont-Ferrand, France
- Université Clermont Auvergne, INRA, UNH, 63000, Clermont-Ferrand, France
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Picca A, Coelho-Junior HJ, Cesari M, Marini F, Miccheli A, Gervasoni J, Bossola M, Landi F, Bernabei R, Marzetti E, Calvani R. The metabolomics side of frailty: Toward personalized medicine for the aged. Exp Gerontol 2019; 126:110692. [PMID: 31421185 DOI: 10.1016/j.exger.2019.110692] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/24/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022]
Abstract
Frailty encompasses several domains (i.e., metabolic, physical, cognitive). The multisystem derangements underlying frailty pathophysiology, its phenotypic heterogeneity, and the fluctuations of individuals across severity states have hampered a comprehensive appraisal of the condition. Circulating biomarkers emerged as an alleged tool for capturing this complexity and, as proxies for organismal metabolic changes, may hold the advantages of: 1) supporting diagnosis, 2) tracking the progression, 3) assisting healthcare professionals in clinical and therapeutic decision-making, and 4) verifying the efficacy of an intervention before measurable clinical manifestations occur. Among available analytical tools, metabolomics are able to identify and quantify the (ideally) whole repertoire of small molecules in biological matrices (i.e., cells, tissues, and biological fluids). Results of metabolomics analysis may define the final output of genome-environment interactions at the individual level. This entire collection of metabolites is called "metabolome" and is highly dynamic. Here, we discuss how monitoring the dynamics of metabolic profiles may provide a read-out of the environmental and clinical disturbances affecting cell homeostasis in frailty-associated conditions.
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Affiliation(s)
- Anna Picca
- Università Cattolica del Sacro Cuore, Institute of Internal Medicine and Geriatrics, 00168 Rome, Italy; Fondazione Policlinico Universitario "Agostino Gemelli" IRCCS, 00168 Rome, Italy
| | - Hélio José Coelho-Junior
- Università Cattolica del Sacro Cuore, Institute of Internal Medicine and Geriatrics, 00168 Rome, Italy; Applied Kinesiology Laboratory-LCA, School of Physical Education, University of Campinas, 13.083-851 Campinas, SP, Brazil
| | - Matteo Cesari
- Department of Clinical Sciences and Community Health, Università di Milano, 20122 Milan, Italy; Geriatric Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Federico Marini
- Department of Chemistry, Sapienza Università di Roma, 00168 Rome, Italy
| | - Alfredo Miccheli
- Department of Chemistry, Sapienza Università di Roma, 00168 Rome, Italy
| | - Jacopo Gervasoni
- Università Cattolica del Sacro Cuore, Institute of Internal Medicine and Geriatrics, 00168 Rome, Italy; Fondazione Policlinico Universitario "Agostino Gemelli" IRCCS, 00168 Rome, Italy
| | - Maurizio Bossola
- Università Cattolica del Sacro Cuore, Institute of Internal Medicine and Geriatrics, 00168 Rome, Italy; Fondazione Policlinico Universitario "Agostino Gemelli" IRCCS, 00168 Rome, Italy
| | - Francesco Landi
- Università Cattolica del Sacro Cuore, Institute of Internal Medicine and Geriatrics, 00168 Rome, Italy; Fondazione Policlinico Universitario "Agostino Gemelli" IRCCS, 00168 Rome, Italy
| | - Roberto Bernabei
- Università Cattolica del Sacro Cuore, Institute of Internal Medicine and Geriatrics, 00168 Rome, Italy; Fondazione Policlinico Universitario "Agostino Gemelli" IRCCS, 00168 Rome, Italy.
| | - Emanuele Marzetti
- Fondazione Policlinico Universitario "Agostino Gemelli" IRCCS, 00168 Rome, Italy.
| | - Riccardo Calvani
- Università Cattolica del Sacro Cuore, Institute of Internal Medicine and Geriatrics, 00168 Rome, Italy; Fondazione Policlinico Universitario "Agostino Gemelli" IRCCS, 00168 Rome, Italy
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Mohyuddin A, Hussain D, Fatima B, Athar M, Ashiq MN, Najam-ul-Haq M. Gallic acid functionalized UiO-66 for the recovery of ribosylated metabolites from human urine samples. Talanta 2019; 201:23-32. [DOI: 10.1016/j.talanta.2019.03.072] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/17/2019] [Accepted: 03/18/2019] [Indexed: 12/12/2022]
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A Quantitative HILIC-MS/MS Assay of the Metabolic Response of Huh-7 Cells Exposed to 2,3,7,8-Tetrachlorodibenzo- p-Dioxin. Metabolites 2019; 9:metabo9060118. [PMID: 31226775 PMCID: PMC6631636 DOI: 10.3390/metabo9060118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/11/2019] [Accepted: 06/13/2019] [Indexed: 01/05/2023] Open
Abstract
A hydrophilic interaction liquid chromatography (HILIC)–ultra high-pressure liquid chromatography (UHPLC) coupled with tandem mass spectrometry (MS/MS) method was developed and applied to profile metabolite changes in human Huh-7 cells exposed to the potent aryl hydrocarbon receptor (AHR) ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Comparisons of sensitivity (limit of detection as low as 0.01 µM) and reproducibility (84% of compounds had an interday relative standard deviation (RSD) less than 10.0%; 83% of compounds had an intraday RSD less than 15.0%) were assessed for all the metabolites. The exposure of Huh-7 cells to the hepatotoxic carcinogen TCDD at low doses (1 nM and 10 nM for 4 h and 24 h, respectively) was reflected by the disturbance of amino acid metabolism, energy metabolism (glycolysis, TCA cycle), and nucleic acid metabolism. TCDD caused a significant decrease in amino acids such as serine, alanine, and proline while promoting an increase in arginine levels with 24 h treatment. Energy metabolism intermediates such as phosphoenolpyruvate and acetyl–CoA and nucleosides such as UMP, XMP, and CMP were also markedly decreased. These results support the application of HILIC–UHPLC–MS/MS for robust and reliable analysis of the cellular response to environmentally relevant toxicants at lower doses.
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Lécuyer L, Dalle C, Lyan B, Demidem A, Rossary A, Vasson MP, Petera M, Lagree M, Ferreira T, Centeno D, Galan P, Hercberg S, Deschasaux M, Partula V, Srour B, Latino-Martel P, Kesse-Guyot E, Druesne-Pecollo N, Durand S, Pujos-Guillot E, Touvier M. Plasma Metabolomic Signatures Associated with Long-term Breast Cancer Risk in the SU.VI.MAX Prospective Cohort. Cancer Epidemiol Biomarkers Prev 2019; 28:1300-1307. [PMID: 31164347 DOI: 10.1158/1055-9965.epi-19-0154] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/12/2019] [Accepted: 05/28/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Breast cancer is a major cause of death in occidental women. The role of metabolism in breast cancer etiology remains unclear. Metabolomics may help to elucidate novel biological pathways and identify new biomarkers to predict breast cancer long before symptoms appear. The aim of this study was to investigate whether untargeted metabolomic signatures from blood draws of healthy women could contribute to better understand and predict the long-term risk of developing breast cancer. METHODS A nested case-control study was conducted within the SU.VI.MAX prospective cohort (13 years of follow-up) to analyze baseline plasma samples of 211 incident breast cancer cases and 211 matched controls by LC/MS. Multivariable conditional logistic regression models were computed. RESULTS A total of 3,565 ions were detected and 1,221 were retained for statistical analysis. A total of 73 ions were associated with breast cancer risk (P < 0.01; FDR ≤ 0.2). Notably, we observed that a lower plasma level of O-succinyl-homoserine (OR = 0.70, 95%CI = [0.55-0.89]) and higher plasma levels of valine/norvaline [1.45 (1.15-1.83)], glutamine/isoglutamine [1.33 (1.07-1.66)], 5-aminovaleric acid [1.46 (1.14-1.87)], phenylalanine [1.43 (1.14-1.78)], tryptophan [1.40 (1.10-1.79)], γ-glutamyl-threonine [1.39 (1.09-1.77)], ATBC [1.41 (1.10-1.79)], and pregnene-triol sulfate [1.38 (1.08-1.77)] were associated with an increased risk of developing breast cancer during follow-up.Conclusion: Several prediagnostic plasmatic metabolites were associated with long-term breast cancer risk and suggested a role of microbiota metabolism and environmental exposure. IMPACT After confirmation in other independent cohort studies, these results could help to identify healthy women at higher risk of developing breast cancer in the subsequent decade and to propose a better understanding of the complex mechanisms involved in its etiology.
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Affiliation(s)
- Lucie Lécuyer
- Sorbonne Paris Cité Epidemiology and Statistics Research Center (CRESS), French National Institute of Health and Medical Research (Inserm) U1153, French National Institute for Agricultural Research (Inra) U1125, French National Conservatory of Arts and Crafts (Cnam), Paris 13 University, Nutritional Epidemiology Research Team (EREN), Bobigny, France.
| | - Céline Dalle
- Clermont Auvergne University, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Bernard Lyan
- Clermont Auvergne University, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Aicha Demidem
- Clermont Auvergne University, INRA, UMR 1019, Human Nutrition Unit (UNH), CRNH Auvergne, Cellular Micro-Environment, Immunomodulation and Nutrition (ECREIN), Clermont-Ferrand, France
| | - Adrien Rossary
- Clermont Auvergne University, INRA, UMR 1019, Human Nutrition Unit (UNH), CRNH Auvergne, Cellular Micro-Environment, Immunomodulation and Nutrition (ECREIN), Clermont-Ferrand, France
| | - Marie-Paule Vasson
- Clermont Auvergne University, INRA, UMR 1019, Human Nutrition Unit (UNH), CRNH Auvergne, Cellular Micro-Environment, Immunomodulation and Nutrition (ECREIN), Clermont-Ferrand, France.,Anticancer Center Jean-Perrin, CHU Clermont-Ferrand, France
| | - Mélanie Petera
- Clermont Auvergne University, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Marie Lagree
- Clermont Auvergne University, Institut de Chimie de Clermont-Ferrand, Plateforme d'Exploration du Métabolisme, MetaboHUB-Clermont, BP 80026, Aubière, France
| | - Thomas Ferreira
- Clermont Auvergne University, INRA, UMR 1019, Human Nutrition Unit (UNH), CRNH Auvergne, Cellular Micro-Environment, Immunomodulation and Nutrition (ECREIN), Clermont-Ferrand, France
| | - Delphine Centeno
- Clermont Auvergne University, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Pilar Galan
- Sorbonne Paris Cité Epidemiology and Statistics Research Center (CRESS), French National Institute of Health and Medical Research (Inserm) U1153, French National Institute for Agricultural Research (Inra) U1125, French National Conservatory of Arts and Crafts (Cnam), Paris 13 University, Nutritional Epidemiology Research Team (EREN), Bobigny, France
| | - Serge Hercberg
- Sorbonne Paris Cité Epidemiology and Statistics Research Center (CRESS), French National Institute of Health and Medical Research (Inserm) U1153, French National Institute for Agricultural Research (Inra) U1125, French National Conservatory of Arts and Crafts (Cnam), Paris 13 University, Nutritional Epidemiology Research Team (EREN), Bobigny, France.,Public Health Department, Avicenne Hospital, Bobigny, France
| | - Mélanie Deschasaux
- Sorbonne Paris Cité Epidemiology and Statistics Research Center (CRESS), French National Institute of Health and Medical Research (Inserm) U1153, French National Institute for Agricultural Research (Inra) U1125, French National Conservatory of Arts and Crafts (Cnam), Paris 13 University, Nutritional Epidemiology Research Team (EREN), Bobigny, France
| | - Valentin Partula
- Sorbonne Paris Cité Epidemiology and Statistics Research Center (CRESS), French National Institute of Health and Medical Research (Inserm) U1153, French National Institute for Agricultural Research (Inra) U1125, French National Conservatory of Arts and Crafts (Cnam), Paris 13 University, Nutritional Epidemiology Research Team (EREN), Bobigny, France
| | - Bernard Srour
- Sorbonne Paris Cité Epidemiology and Statistics Research Center (CRESS), French National Institute of Health and Medical Research (Inserm) U1153, French National Institute for Agricultural Research (Inra) U1125, French National Conservatory of Arts and Crafts (Cnam), Paris 13 University, Nutritional Epidemiology Research Team (EREN), Bobigny, France
| | - Paule Latino-Martel
- Sorbonne Paris Cité Epidemiology and Statistics Research Center (CRESS), French National Institute of Health and Medical Research (Inserm) U1153, French National Institute for Agricultural Research (Inra) U1125, French National Conservatory of Arts and Crafts (Cnam), Paris 13 University, Nutritional Epidemiology Research Team (EREN), Bobigny, France
| | - Emmanuelle Kesse-Guyot
- Sorbonne Paris Cité Epidemiology and Statistics Research Center (CRESS), French National Institute of Health and Medical Research (Inserm) U1153, French National Institute for Agricultural Research (Inra) U1125, French National Conservatory of Arts and Crafts (Cnam), Paris 13 University, Nutritional Epidemiology Research Team (EREN), Bobigny, France
| | - Nathalie Druesne-Pecollo
- Sorbonne Paris Cité Epidemiology and Statistics Research Center (CRESS), French National Institute of Health and Medical Research (Inserm) U1153, French National Institute for Agricultural Research (Inra) U1125, French National Conservatory of Arts and Crafts (Cnam), Paris 13 University, Nutritional Epidemiology Research Team (EREN), Bobigny, France
| | - Stéphanie Durand
- Clermont Auvergne University, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Estelle Pujos-Guillot
- Clermont Auvergne University, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Mathilde Touvier
- Sorbonne Paris Cité Epidemiology and Statistics Research Center (CRESS), French National Institute of Health and Medical Research (Inserm) U1153, French National Institute for Agricultural Research (Inra) U1125, French National Conservatory of Arts and Crafts (Cnam), Paris 13 University, Nutritional Epidemiology Research Team (EREN), Bobigny, France
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Zhou J, Tang L, Wang JS. Assessment of the adverse impacts of aflatoxin B 1 on gut-microbiota dependent metabolism in F344 rats. CHEMOSPHERE 2019; 217:618-628. [PMID: 30447610 DOI: 10.1016/j.chemosphere.2018.11.044] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 11/04/2018] [Accepted: 11/05/2018] [Indexed: 06/09/2023]
Abstract
The adverse impacts of AFB1 on gut-microbiota dependent metabolism in F344 rats were assessed via ultra-high performance liquid chromatography (UHPLC)-profiling and UHPLC-mass spectrometry (MS) metabolomic analyses. UHPLC-profiling analysis found 1100 raw peaks from the fecal samples collected at week 4, of which 335 peaks showed peak shape qualified for quantitation. A total of 24, 40 and 71 peaks were significantly decreased (>2-fold, p < 0.05) among the exposure groups treated with 5, 25, and 75 μg AFB1 kg-1 body weight (B. W.), respectively. Supervised orthogonal partial least squares projection to latent structures-discriminant analysis revealed 11 differential peaks that may be used to predict AFB1-induced adverse changes of the metabolites. UHPLC-MS based metabolomic analysis discovered 494 features that were significantly altered by AFB1, and 234 of them were imputatively identified using Human Metabolome Data Base (HMDB). Metabolite set enrichment analysis showed that the highly disrupted metabolic pathways were: protein biosynthesis, pantothenate and CoA biosynthesis, betaine metabolism, cysteine metabolism, and methionine metabolism. Eight features were rated as indicative metabolites for AFB1 exposure: 3-decanol, xanthylic acid, norspermidine, nervonyl carnitine, pantothenol, threitol, 2-hexanoyl carnitine, and 1-nitrohexane. These data suggest that AFB1 could significantly reduce the variety of nutrients in gut and disrupt a number of gut-microbiota dependent metabolic pathways, which may contribute to the AFB1-associated stunted growth, liver diseases and the immune toxic effects that have been observed in animal models and human populations.
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Affiliation(s)
- Jun Zhou
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA 30602, United States; Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602, United States
| | - Lili Tang
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA 30602, United States; Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602, United States
| | - Jia-Sheng Wang
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA 30602, United States; Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA 30602, United States.
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Ramautar R. Sheathless Capillary Electrophoresis-Mass Spectrometry for the Profiling of Charged Metabolites in Biological Samples. Methods Mol Biol 2019; 1738:183-192. [PMID: 29654590 DOI: 10.1007/978-1-4939-7643-0_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Capillary electrophoresis (CE) is well suited for the profiling of highly polar and charged metabolites as compounds are separated on the basis of their charge-to-size ratio. The protocol presented here is based on using a recently developed sheathless interfacing design, i.e., a porous tip interface, for coupling CE to electrospray ionization mass spectrometry (MS). It is demonstrated that sheathless CE-MS employing a bare fused-silica capillary at low-pH separation conditions can be used for the profiling of both cationic and anionic metabolites by only switching the MS detection and electrophoretic separation voltage polarity. The proposed sheathless CE-MS protocol allows efficient and sensitive profiles to be obtained for a broad array of charged metabolites, including amino acids, organic acids, nucleotides, and sugar phosphates, in various biological samples, such as urine and extracts of the glioblastoma cell line.
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Affiliation(s)
- Rawi Ramautar
- Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands.
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Pujos-Guillot E, Pétéra M, Jacquemin J, Centeno D, Lyan B, Montoliu I, Madej D, Pietruszka B, Fabbri C, Santoro A, Brzozowska A, Franceschi C, Comte B. Identification of Pre-frailty Sub-Phenotypes in Elderly Using Metabolomics. Front Physiol 2019; 9:1903. [PMID: 30733683 PMCID: PMC6353829 DOI: 10.3389/fphys.2018.01903] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 12/18/2018] [Indexed: 01/14/2023] Open
Abstract
Aging is a dynamic process depending on intrinsic and extrinsic factors and its evolution is a continuum of transitions, involving multifaceted processes at multiple levels. It is recognized that frailty and sarcopenia are shared by the major age-related diseases thus contributing to elderly morbidity and mortality. Pre-frailty is still not well understood but it has been associated with global imbalance in several physiological systems, including inflammation, and in nutrition. Due to the complex phenotypes and underlying pathophysiology, the need for robust and multidimensional biomarkers is essential to move toward more personalized care. The objective of the present study was to better characterize the complexity of pre-frailty phenotype using untargeted metabolomics, in order to identify specific biomarkers, and study their stability over time. The approach was based on the NU-AGE project (clinicaltrials.gov, NCT01754012) that regrouped 1,250 free-living elderly people (65–79 y.o., men and women), free of major diseases, recruited within five European centers. Half of the volunteers were randomly assigned to an intervention group (1-year Mediterranean type diet). Presence of frailty was assessed by the criteria proposed by Fried et al. (2001). In this study, a sub-cohort consisting in 212 subjects (pre-frail and non-frail) from the Italian and Polish centers were selected for untargeted serum metabolomics at T0 (baseline) and T1 (follow-up). Univariate statistical analyses were performed to identify discriminant metabolites regarding pre-frailty status. Predictive models were then built using linear logistic regression and ROC curve analyses were used to evaluate multivariate models. Metabolomics enabled to discriminate sub-phenotypes of pre-frailty both at the gender level and depending on the pre-frailty progression and reversibility. The best resulting models included four different metabolites for each gender. They showed very good prediction capacity with AUCs of 0.93 (95% CI = 0.87–1) and 0.94 (95% CI = 0.87–1) for men and women, respectively. Additionally, early and/or predictive markers of pre-frailty were identified for both genders and the gender specific models showed also good performance (three metabolites; AUC = 0.82; 95% CI = 0.72–0.93) for men and very good for women (three metabolites; AUC = 0.92; 95% CI = 0.86–0.99). These results open the door, through multivariate strategies, to a possibility of monitoring the disease progression over time at a very early stage.
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Affiliation(s)
- Estelle Pujos-Guillot
- Université Clermont Auvergne, Institut National de la Recherche Agronomique, Unité de Nutrition Humaine, Centre Auvergne Rhône Alpes, Clermont-Ferrand, France.,Université Clermont Auvergne, Institut National de la Recherche Agronomique, Unité de Nutrition Humaine, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Mélanie Pétéra
- Université Clermont Auvergne, Institut National de la Recherche Agronomique, Unité de Nutrition Humaine, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Jérémie Jacquemin
- Université Clermont Auvergne, Institut National de la Recherche Agronomique, Unité de Nutrition Humaine, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Delphine Centeno
- Université Clermont Auvergne, Institut National de la Recherche Agronomique, Unité de Nutrition Humaine, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Bernard Lyan
- Université Clermont Auvergne, Institut National de la Recherche Agronomique, Unité de Nutrition Humaine, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
| | - Ivan Montoliu
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Dawid Madej
- Department of Human Nutrition, Warsaw University of Life Sciences - Szkoła Główna Gospodarstwa Wiejskiego, Warsaw, Poland
| | - Barbara Pietruszka
- Department of Human Nutrition, Warsaw University of Life Sciences - Szkoła Główna Gospodarstwa Wiejskiego, Warsaw, Poland
| | - Cristina Fabbri
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Aurelia Santoro
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.,Interdepartmental Center "L. Galvani", University of Bologna, Bologna, Italy
| | - Anna Brzozowska
- Department of Human Nutrition, Warsaw University of Life Sciences - Szkoła Główna Gospodarstwa Wiejskiego, Warsaw, Poland
| | | | - Blandine Comte
- Université Clermont Auvergne, Institut National de la Recherche Agronomique, Unité de Nutrition Humaine, Centre Auvergne Rhône Alpes, Clermont-Ferrand, France
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Zhang W, Hankemeier T, Ramautar R. Capillary Electrophoresis-Mass Spectrometry for Metabolic Profiling of Biomass-Limited Samples. Methods Mol Biol 2019; 1972:165-172. [PMID: 30847790 DOI: 10.1007/978-1-4939-9213-3_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Capillary electrophoresis-mass spectrometry (CE-MS) is a strong separation technique for the highly efficient and selective analysis of polar and charged metabolites in biological samples. The CE approach is especially suited for the analysis of limited sample amounts due to its nanoliter injections from only a few microliters of material in the sample injection vial. In this protocol, a CE-MS strategy is outlined for the profiling of cationic metabolites in biomass-limited samples using a small amount of human hepatocellular carcinoma (HepG2) cells as a model system. By employing a sheathless interfacing design for coupling CE to MS, it is shown that information-rich profiles for cationic metabolites can be obtained when working with a starting amount of 10,000 HepG2 cells and even lower. Overall, the proposed CE-MS-based analytical workflow may be considered a useful tool for biomass-limited metabolomics studies.
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Affiliation(s)
- Wei Zhang
- Biomedical Microscale Analytics, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Thomas Hankemeier
- Biomedical Microscale Analytics, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Rawi Ramautar
- Biomedical Microscale Analytics, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands.
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Zhang W, Guled F, Hankemeier T, Ramautar R. Utility of sheathless capillary electrophoresis-mass spectrometry for metabolic profiling of limited sample amounts. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1105:10-14. [DOI: 10.1016/j.jchromb.2018.12.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/17/2018] [Accepted: 12/04/2018] [Indexed: 12/01/2022]
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Sasaki K, Sagawa H, Suzuki M, Yamamoto H, Tomita M, Soga T, Ohashi Y. Metabolomics Platform with Capillary Electrophoresis Coupled with High-Resolution Mass Spectrometry for Plasma Analysis. Anal Chem 2018; 91:1295-1301. [PMID: 30500154 DOI: 10.1021/acs.analchem.8b02994] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Metabolome analysis using capillary electrophoresis (CE) coupled with high-resolution mass spectrometry (HRMS) has the potential to improve coverage of metabolite detection because of its high selectivity and sensitivity. Configuration of the interface between CE and HRMS to meet the ground connection is essential for enabling independent regulation of the electrical currents in the CE and electrospray field. In the present study, we applied an electrospray-ionization adapter equipped with a grounded nebulizer to CE-HRMS and tested the analytical performance for 34 charged compounds. The extracted-ion electropherograms, consisting of seven sets of isomers, showed reasonable peak shapes and separation for the annotation of each metabolite. The levels of 34 target analytes in a standard mixture were determined with a dynamic range of at least 102, maintaining linearity with r2 > 0.9. The repeatability and intermediate precision above the lower limit of quantification showed the relative standard deviation to be lower than 20%. In the spike-recovery experiment, 27 of the 34 metabolites in plasma extract were recovered at a rate of 80 to 120%, suggesting high accuracy. Furthermore, we assessed the feasibility of our platform in metabolome analysis using human-plasma extract. The results showed successful detection of 270 metabolites, indicating the potential of our platform to yield higher coverage of the metabolome. In addition, analysis of dilution integrity demonstrated the quantitative ability of metabolome analysis with CE-HRMS, although the existence of saturation or matrix effects were seen in the case of 33 of the metabolites. This study indicates that our platform has great potential for large-scale metabolome analysis of plasma for biological studies and clinical biomarker screening.
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Affiliation(s)
- Kazunori Sasaki
- Human Metabolome Technologies Inc. , 246-2 Mizukami , Kakuganji, Tsuruoka , Yamagata 997-0052 , Japan.,Institute for Advanced Biosciences , Keio University , 246-2 Mizukami , Kakuganji, Tsuruoka , Yamagata 997-0052 , Japan
| | - Hitoshi Sagawa
- Human Metabolome Technologies Inc. , 246-2 Mizukami , Kakuganji, Tsuruoka , Yamagata 997-0052 , Japan
| | - Makoto Suzuki
- Human Metabolome Technologies Inc. , 246-2 Mizukami , Kakuganji, Tsuruoka , Yamagata 997-0052 , Japan
| | - Hiroyuki Yamamoto
- Human Metabolome Technologies Inc. , 246-2 Mizukami , Kakuganji, Tsuruoka , Yamagata 997-0052 , Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences , Keio University , 246-2 Mizukami , Kakuganji, Tsuruoka , Yamagata 997-0052 , Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences , Keio University , 246-2 Mizukami , Kakuganji, Tsuruoka , Yamagata 997-0052 , Japan
| | - Yoshiaki Ohashi
- Human Metabolome Technologies Inc. , 246-2 Mizukami , Kakuganji, Tsuruoka , Yamagata 997-0052 , Japan
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Kennedy AD, Wittmann BM, Evans AM, Miller LAD, Toal DR, Lonergan S, Elsea SH, Pappan KL. Metabolomics in the clinic: A review of the shared and unique features of untargeted metabolomics for clinical research and clinical testing. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:1143-1154. [PMID: 30242936 DOI: 10.1002/jms.4292] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/10/2018] [Accepted: 09/17/2018] [Indexed: 06/08/2023]
Abstract
Metabolomics is the untargeted measurement of the metabolome, which is composed of the complement of small molecules detected in a biological sample. As such, metabolomic analysis produces a global biochemical phenotype. It is a technology that has been utilized in the research setting for over a decade. The metabolome is directly linked to and is influenced by genetics, epigenetics, environmental factors, and the microbiome-all of which affect health. Metabolomics can be applied to human clinical diagnostics and to other fields such as veterinary medicine, nutrition, exercise, physiology, agriculture/plant biochemistry, and toxicology. Applications of metabolomics in clinical testing are emerging, but several aspects of its use as a clinical test differ from applications focused on research or biomarker discovery and need to be considered for metabolomics clinical test data to have optimum impact, be meaningful, and be used responsibly. In this review, we deconstruct aspects and challenges of metabolomics for clinical testing by illustrating the significance of test design, accurate and precise data acquisition, quality control, data processing, n-of-1 comparison to a reference population, and biochemical pathway analysis. We describe how metabolomics technology is integral to defining individual biochemical phenotypes, elaborates on human health and disease, and fits within the precision medicine landscape. Finally, we conclude by outlining some future steps needed to bring metabolomics into the clinical space and to be recognized by the broader medical and regulatory fields.
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Affiliation(s)
| | | | | | | | | | | | - Sarah H Elsea
- Department of Molecular and Human Genetics and Baylor Genetics, Baylor College of Medicine, Houston, TX, USA
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Ramautar R, Somsen GW, de Jong GJ. CE-MS for metabolomics: Developments and applications in the period 2016-2018. Electrophoresis 2018; 40:165-179. [PMID: 30232802 PMCID: PMC6586046 DOI: 10.1002/elps.201800323] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/09/2018] [Accepted: 09/10/2018] [Indexed: 12/16/2022]
Abstract
In the field of metabolomics, CE-MS is now recognized as a strong analytical technique for the analysis of (highly) polar and charged metabolites in a wide range of biological samples. Over the past few years, significant attention has been paid to the design and improvement of CE-MS approaches for (large-scale) metabolic profiling studies and for establishing protocols in order to further expand the role of CE-MS in metabolomics. In this paper, which is a follow-up of a previous review paper covering the years 2014-2016 (Electrophoresis 2017, 38, 190-202), main advances in CE-MS approaches for metabolomics studies are outlined covering the literature from July 2016 to June 2018. Aspects like developments in interfacing designs and data analysis tools for improving the performance of CE-MS for metabolomics are discussed. Representative examples highlight the utility of CE-MS in the fields of biomedical, clinical, microbial, and plant metabolomics. A complete overview of recent CE-MS-based metabolomics studies is given in a table, which provides information on sample type and pretreatment, capillary coatings and MS detection mode. Finally, some general conclusions and perspectives are given.
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Affiliation(s)
- Rawi Ramautar
- Biomedical Microscale Analytics, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Govert W Somsen
- Division of BioAnalytical Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gerhardus J de Jong
- Biomolecular Analysis, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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Crabtree GW, Gogos JA. Role of Endogenous Metabolite Alterations in Neuropsychiatric Disease. ACS Chem Neurosci 2018; 9:2101-2113. [PMID: 30044078 DOI: 10.1021/acschemneuro.8b00145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The potential role in neuropsychiatric disease risk arising from alterations and derangements of endogenous small-molecule metabolites remains understudied. Alterations of endogenous metabolite concentrations can arise in multiple ways. Marked derangements of single endogenous small-molecule metabolites are found in a large group of rare genetic human diseases termed "inborn errors of metabolism", many of which are associated with prominent neuropsychiatric symptomology. Whether such metabolites act neuroactively to directly lead to distinct neural dysfunction has been frequently hypothesized but rarely demonstrated unequivocally. Here we discuss this disease concept in the context of our recent findings demonstrating that neural dysfunction arising from accumulation of the schizophrenia-associated metabolite l-proline is due to its structural mimicry of the neurotransmitter GABA that leads to alterations in GABA-ergic short-term synaptic plasticity. For cases in which a similar direct action upon neurotransmitter binding sites is suspected, we lay out a systematic approach that can be extended to assessing the potential disruptive action of such candidate disease metabolites. To address the potentially important and broader role in neuropsychiatric disease, we also consider whether the more subtle yet more ubiquitous variations in endogenous metabolites arising from natural allelic variation may likewise contribute to disease risk but in a more complex and nuanced manner.
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Affiliation(s)
- Gregg W. Crabtree
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, New York 10032, United States
- Zuckerman Mind Brain Behavior Institute, New York, New York 10025, United States
| | - Joseph A. Gogos
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, New York 10032, United States
- Zuckerman Mind Brain Behavior Institute, New York, New York 10025, United States
- Department of Neuroscience, Columbia University Medical Center, New York, New York 10032, United States
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Jedlicka LDL, Silva JDC, Balbino AM, Neto GB, Furtado DZS, da Silva HDT, Cavalcanti FDBC, van der Heijden KM, Penatti CAA, Bechara EJH, Assunção NA. Effects of Diacetyl Flavoring Exposure in Mice Metabolism. BIOMED RESEARCH INTERNATIONAL 2018; 2018:9875319. [PMID: 30065948 PMCID: PMC6051334 DOI: 10.1155/2018/9875319] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/27/2018] [Accepted: 05/08/2018] [Indexed: 01/06/2023]
Abstract
Diacetyl is a flavoring that imparts a buttery flavor to foods, but the use or exposure to diacetyl has been related to some diseases. We investigated the effect of oral intake of diacetyl in male and female C57/Bl mice. We performed a target metabolomics assay using ultraperformance liquid chromatography paired with triple quadrupole mass spectrometry (UPLC-MS/MS) for the determination and quantification of plasmatic metabolites. We observed alterations in metabolites present in the urea and tricarboxylic acid (TCA) cycles. Peroxynitrite plasmatic levels were evaluated by a colorimetric method, final activity of superoxide dismutase (SOD) was evaluated by an enzymatic method, and mouse behavior was evaluated. Majority of the assay showed differences between control and treatment groups, as well as between genders. This may indicate the involvement of sex hormones in the regulation of a normal metabolic profile, and the implication of sex differences in metabolite disease response.
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Affiliation(s)
- Letícia Dias Lima Jedlicka
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, SP, Brazil
- Instituto de Estudos em Saúde e Biológicas, Universidade Federal do Sul e Sudeste do Pará, Marabá, PA, Brazil
| | | | - Aleksandro Martins Balbino
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, SP, Brazil
| | - Giuseppe Bruno Neto
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, SP, Brazil
| | | | | | | | | | | | | | - Nilson Antonio Assunção
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, SP, Brazil
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50
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Gibson CL, Codreanu SG, Schrimpe-Rutledge AC, Retzlaff CL, Wright J, Mortlock DP, Sherrod SD, McLean JA, Blakely RD. Global untargeted serum metabolomic analyses nominate metabolic pathways responsive to loss of expression of the orphan metallo β-lactamase, MBLAC1. Mol Omics 2018; 14:142-155. [PMID: 29868674 PMCID: PMC6015503 DOI: 10.1039/c7mo00022g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The C. elegans gene swip-10 encodes an orphan metallo β-lactamase that genetic studies indicate is vital for limiting neuronal excitability and viability. Sequence analysis indicates that the mammalian gene Mblac1 is the likely ortholog of swip-10, with greatest sequence identity localized to the encoded protein's single metallo β-lactamase domain. The substrate for the SWIP-10 protein remains unknown and to date no functional roles have been ascribed to MBLAC1, though we have shown that the protein binds the neuroprotective β-lactam antibiotic, ceftriaxone. To gain insight into the functional role of MBLAC1 in vivo, we used CRISPR/Cas9 methods to disrupt N-terminal coding sequences of the mouse Mblac1 gene, resulting in a complete loss of protein expression in viable, homozygous knockout (KO) animals. Using serum from both WT and KO mice, we performed global, untargeted metabolomic analyses, resolving small molecules via hydrophilic interaction chromatography (HILIC) based ultra-performance liquid chromatography, coupled to mass spectrometry (UPLC-MS/MS). Unsupervised principal component analysis reliably segregated the metabolomes of MBLAC1 KO and WT mice, with 92 features subsequently nominated as significantly different by ANOVA, and for which we made tentative and putative metabolite assignments. Bioinformatic analyses of these molecules nominate validated pathways subserving bile acid biosynthesis and linoleate metabolism, networks known to be responsive to metabolic and oxidative stress. Our findings lead to hypotheses that can guide future targeted studies seeking to identify the substrate for MBLAC1 and how substrate hydrolysis supports the neuroprotective actions of ceftriaxone.
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Affiliation(s)
- Chelsea L. Gibson
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Jupiter FL, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN USA
| | - Simona G. Codreanu
- Department of Chemistry, Vanderbilt University, Nashville, TN USA
- Center for Innovative Technology, Vanderbilt University, Nashville, TN USA
| | - Alexandra C. Schrimpe-Rutledge
- Department of Chemistry, Vanderbilt University, Nashville, TN USA
- Center for Innovative Technology, Vanderbilt University, Nashville, TN USA
| | - Cassandra L. Retzlaff
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Jupiter FL, USA
| | - Jane Wright
- Department of Pharmacology, Vanderbilt University, Nashville, TN USA
| | - Doug P. Mortlock
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN USA
| | - Stacy D. Sherrod
- Department of Chemistry, Vanderbilt University, Nashville, TN USA
- Center for Innovative Technology, Vanderbilt University, Nashville, TN USA
| | - John A. McLean
- Department of Chemistry, Vanderbilt University, Nashville, TN USA
- Center for Innovative Technology, Vanderbilt University, Nashville, TN USA
| | - Randy D. Blakely
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Jupiter FL, USA
- Brain Institute, Florida Atlantic University, Jupiter FL, USA
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